NEWS

---

BoutrosLab.plotting.general 7.1.2 (2024-10-04)

Changed

• Improved "sample.order" argument checking
• Updated NEWS to Markdown NEWS.md format
• Cleaned the C++ namespace by using R_ versions of Free, Calloc, and Realloc

BoutrosLab.plotting.general 7.1.1

Changed

• Improved documentation for type parameter in create.scatterplot

Fixed

• Fix typo in README
• Update package manual for CRAN standards

BoutrosLab.plotting.general 7.1.0 (2023-10-28)

Added

• Add testthat framework for package tests
• Use mockr for unit testing
• Improve documentation for automatic axis scaling in:
  • create.scatterplot
  • create.boxplot
  • create.manhattanplot
  • create.hexbinplot

BoutrosLab.plotting.general 7.0.10 (2023-10-24)

Changed

• Add deprecation warning for test file in preparation for using testthat in the v8.0.0 release

BoutrosLab.plotting.general 7.0.9

Changed

• Run R CMD check GitHub action weekly and with manual dispatch
• Updated GitHub links to use new "package" prefix

Removed

• Remove unnecessary package manual file

BoutrosLab.plotting.general 7.0.8 (2023-05-30)

Changed

• Change name of print.to.file() to export.to.file() to avoid naming conflict with S3 method print()

BoutrosLab.plotting.general 7.0.7

Changed

• Expose panel.text arguments for text.above.bar options in create.barplot
• Remove duplicated code in print.multipanel
• Update format of CRAN links
• Add default label locations for continuous legends

Fixed

• Fix error with expressions in main for multipanelplots

Removed

• Remove outdated plotting data storage code

BoutrosLab.plotting.general 7.0.6

Added

• Add github PR template

Changed

• Move CICD workflow from Dockerhub to GitHub packages
• Add text support for create.histogram
• Remove axis labels with axis.lab = NULL in create.boxplot for consistent behavior with other plot types

Fixed

• Fix ylab.axis.padding parameter in create.histogram
• Fix error when using expressions in multipanelplot labels and main

BoutrosLab.plotting.general 7.0.5 (2023-01-06)

Changed

• Fix typo in man/create.violinplot.Rd
• Add alpha parameter to create.boxplot
• Added GitHub repo to package description
• Correctly sort horizontal barplot
• Remove Makefile
• Replaced string class comparison with is()

Fixed

• Fix NEWS format
• Fix ## Fixed with persisted plotting function output in examples

BoutrosLab.plotting.general 7.0.4

Changed

• Fix border specification in create.polygonplot

BoutrosLab.plotting.general 7.0.3 (2022-03-18)

Changed

• Update .Rbuildignore to match lab R standards

BoutrosLab.plotting.general 7.0.2

Fixed

• Add type comparisons for class name comparisons

BoutrosLab.plotting.general 7.0.1

Fixed

• Fix object protection issue in distance.c

BoutrosLab.plotting.general 7.0.0

Changed

• Renamed ks.test.critical.value() function to critical.value.ks.test() to resolve naming conflict with S3 generic ks.test() from base R stats package.

Fixed

• Fix issue when specifying multiple line-widths in create.polygonplot()

BoutrosLab.plotting.general 6.1.0

Changed

• Add option to use dots in a legend instead of default rectangles
• Enable create.boxplot to print different text label on each panel

Fixed

• Fixed inconsistent grouping of point colours in create.boxplot
• Account for case where only one colour is passed to create.heatmap

BoutrosLab.plotting.general 6.0.3 (2021-01-25)

Changed

• Only use cairo in the examples for covariates.grob and legend.grob if capabilities('cairo') is true.

BoutrosLab.plotting.general 6.0.2 (2021-01-11)

Changed

• Depends versions: R (>= 3.5.0), lattice (>= 0.20-35), latticeExtra (>= 0.6-27), cluster (>= 2.0.0), hexbin (>= 1.27.0)
• Only use cairo when capabilities('cairo') is true to fix CRAN's issue of cairo not being available on M1 Macs

BoutrosLab.plotting.general 6.0.1 (2020-08-05)

Changed

• Added paper's doi to DESCRIPTION

Removed

• Removed use of tocstyle package in PlottingGuide as that is obsolete and failing CRAN's check

BoutrosLab.plotting.general 6.0.0 (2020-04-06)

Changed

• Updated contact email
• Included source code previously imported from BoutrosLab.dist.overload and BoutrosLab.statistics.general
• Fixed resolutions for examples to reduce running time
• Added \donttest{} to examples that took >5 seconds to run
• Examples now output plots to tempdir()

Fixed

• Fixed errors in create.multiplot and create.multipanel that wasn't passing CRAN's check by changing 'is.na' to 'anyNA'
• Fixed errors in create.multiplot that was only checking the first element in a list by using 'is.element' instead of '=='
• Fixed spacing issue in PlottingGuide
• Added stringsAsFactors = TRUE to data.frame() calls in examples (Changes to R-devel in 2020-03-04 changed the defaults)
• Fixed thousands.splits to return a vector instead of a list
• Fixed write.metadata to use double quotes on system calls, correctly show BL.plotting.survival version and consolidate exiftool calls to speed things up
• Fixed CRAN error misuse of package= for PACKAGE=

Removed

• Removed BoutrosLab.utilities::recode.vector calls in examples
• Removed requirements for BoutrosLab.utilities, BoutrosLab.dist.overload, BoutrosLab.statistics.general

BoutrosLab.plotting.general 5.9.8

Changed

• create.hexbinplot: added option to modify the default legend title

BoutrosLab.plotting.general 5.9.7

Fixed

• Fixed an issue regarding warning detection for class of conditioning variable that didn't recognize character input (barplot, boxplot, hexbinplot, scatterplot)

BoutrosLab.plotting.general 5.9.6

Fixed

• Fixed an issue that prevented extra points from plotting correctly in create.polygonplot

BoutrosLab.plotting.general 5.9.5

Changed

• Added warnings when a formula contains a conditioning variable that is an integer/numeric (barplot, boxplot, hexbinplot, scatterplot)
• Changed default xaxis.tck for boxplot to prevent automatic ticks from appearing at top of plot

Fixed

• Force.colour.scheme no longer requires 'x' when return.scheme = TRUE
• Fixed an error in create.scatterplot preventing automatic axis determination when all y == 0 or all y == -N

Removed

• Removed append.footnote.R as it was non-functional with no plans to fix

BoutrosLab.plotting.general 5.9.4

Changed

• Dotmap can now do symmetrical removing of top left half of dotmap

Fixed

• Top covariates in heatmap now have proper defaults

BoutrosLab.plotting.general 5.9.3

Changed

• Updated dependencies to not include as many
• Boxplot now saves all its data (for later use)
• multipanelplot now saves temp plots to temp dir

Fixed

• Default.colours no longer references wrong grey scale colour

BoutrosLab.plotting.general 5.9.2 (2018-04-23)

Changed

• Legend grob for continous legends now auto place themselves -- x and y pos dont do anything anymore
• Print to file will now override previous entries
• Removed printing for individual plot info (too unreliable)

BoutrosLab.plotting.general 5.9.1

Changed

• Multipanel plot now uses tob axis labels too for lining up plots

Fixed

• Multipanel plot now correctly positions plot main labels

BoutrosLab.plotting.general 5.9.0

Changed

• Added code for saving data information and trellis object information to each relevant plot

BoutrosLab.plotting.general 5.8.16

Changed

• Cleaned up the multipanelplot code and ## Changedd the examples

BoutrosLab.plotting.general 5.8.15

Changed

• Made multipanelplot legend/label placement algorithm more optimal

BoutrosLab.plotting.general 5.8.14

Changed

• Now stores data on the mount

Fixed

• Text now passed to panel in seperate list, stopping it from being reset in between plots

BoutrosLab.plotting.general 5.8.13

Changed

• Adjusted polygon plot to work well with roc plot

BoutrosLab.plotting.general 5.8.12

Changed

• Added lollipop plot as an extension of scatterplot

BoutrosLab.plotting.general 5.8.11

Changed

• Added ability to disable factor sorting in relative plots
• Added example to histogram of type change

BoutrosLab.plotting.general 5.8.10

Changed

• Added border colour for histogram bars

BoutrosLab.plotting.general 5.8.9

Changed

• Added inside legend auto finder code

Fixed

• Boxplot addstriplot colour was having issue with multiple boxplots, now works properly

BoutrosLab.plotting.general 5.8.8

Changed

• Updated formatting to match coding standard
• Added inside legends to multipanel plot

Fixed

• Heatmap now accepts both x and y axis covariates

BoutrosLab.plotting.general 5.8.7

Changed

• Updated formatting to match coding standard

BoutrosLab.plotting.general 5.8.6

Changed

• Legend and covariate grobs can now use x and y coordinates

Fixed

• Heatmap using colours must faster
• Legacy settings in multipanel plot now affect all individual plots too

BoutrosLab.plotting.general 5.8.5

Changed

• Force colour scheme now has heteroplasmy fraction and MT annotation

BoutrosLab.plotting.general 5.8.4

Fixed

• Multipanel plot now accepts colorkey and draw key legends
• Get defaults now retrieves ArialMT instead of Arial font (actual name on Linux)

Changed

• Heatmap can now use colours to specify the squares
• Density plot can now add text (like bar/boxplot)

BoutrosLab.plotting.general 5.8.3

Fixed

• Multipanel plot now works with legends from original plots
• Barplot error bars now work with horizontal plots too

Changed

• Heatmap now accepts inside legends and can specify text not based on grid cooridnates

BoutrosLab.plotting.general 5.8.2

Fixed

• Completely reworked how spacing works in multipanel plot -- now creates rectangular grobs instead of using top/left/right/bottom padding

BoutrosLab.plotting.general 5.8.1

Fixed

• Multipanel plot background colour
• Multipanel plot not accepting expression labels
• Multipanel deleting plots main labels
• Heatmap legend layout works properly now

BoutrosLab.plotting.general 5.8.0

Added

• New create.multiplot function (create.multipanelplot)

Fixed

• Auto-axis now gives 5 labels by default instead of 4
• Same.as.matrix can now be applied to create dendrogram outside of heatmap
• Fixed filename error in crete.gif
• Heatmap now loads defaults
• Segplot defaults to bold like rest of plots
• Colours for default dotmap now match the documentation (had to reverse them)

Changed

*pcawg.colours: new and renamed tumour type names added to palette, sv class 'insertion' assigned colour

BoutrosLab.plotting.general 5.7.6

Fixed

• 1D heatmaps now work -- automatically
• Error bars now work properly with grouped bar plots

Changed

• Automatic layout justification for legends (using just arg) for continous legends
• Added helper function for seperating thousands by commas, i.e -> (12345) -> (12,345)
• Merged all the relevent colour functions into force.colour.scheme
• Can now extract dendrograms from a heatmap (only one, and may require manual manipulation)

Fixed

• create.heatmap - grid row/column limits reversed
• Legend.grob - continuous legends produce warnings
• Ytop.rectangle in create.scatterplot() doesn't work properly.
• Remove the old option (retrieve.plot.labels) and merge into (plot.labels.to.retrieve)

Changed

• Merged multiple colour functions (old ones to be ## Removed in next commit)
• Multiple colours of error bars in scatterplot
• Add xaxis.rot.top option to create.multiplot
• Have legends on both the left AND the right for create.heatmap

BoutrosLab.plotting.general 5.7.4

Fixed

• Automatic labels not working for stacked barplots
• Removed log scaling from stacked barplots
• Fixed 1 D heatmap issues

Added

• Search metadata function

BoutrosLab.plotting.general 5.7.3

Changed

• Each plot can put xat/yat = "auto"/"auto.linear"/"auto.log" to get automatic labels

Added

• Pretty axis function -- input data set gives ## Changedd data values and labels

BoutrosLab.plotting.general 5.7.2

Changed

• Can now add border to correlation keys
• Issues around multiplot reseting labels on y axis when x asis labels added solved

Added

• create.gif for creating animated plots

BoutrosLab.plotting.general 5.7.1

Fixed

• Write.plot.R: fixed an error that didn't allow adding additional plots when returning object to screen (when filename = NULL)
• create.barplot.R: fixed a ## Fixed interfering with add.rectangle and ## Removed redundant add.background.shading (repeats add.rectangle functionality)
• Force.colour.scheme: if multiple outputs were requested only one would be returned; now returns a list

Changed

• create.barplot.R: minor improvements to some examples
• Split argument lwd into axes.lwd and border.lwd to be consistent with other functions
• Removed argument remove.all.border.lines as this can now be accomplished with axes.lwd
• Applied code formatting (BL standards)

BoutrosLab.plotting.general 5.7.0

Fixed

• create.violinplot: fixed a ## Fixed in colour functionality; now repeats colours when fewer colours are supplied than there are groups

Changed

• create.hexbinplot: changed argument abline.type to abline.lty to be consistent with other functions
• create.segplot: added warning for specific use case (multiplot fails when a vertical segplot is the first plot)
• create.manhattanplot: changed argument axis.lwd to axes.lwd to be consistent with other functions
• create.hexbinplot, create.histogram, create.manhattanplot, create.polygonplot, create.qqplot.comparison, create.qqplot.fit, create.scatterplot, create.stripplot, create.segplot, create.violinplot, age.categorical.colour, append.footnote: applied code formatting (BL standards)

BoutrosLab.plotting.general 5.6.24

Changed

*create.multiplot: Added functionality to add top x-axis tick labels. Has not been extensively tested.

BoutrosLab.plotting.general 5.6.23

Fixed

*pcawg.colours: fixed ## Fixed that prevented project code colours from being returned.

BoutrosLab.plotting.general 5.6.22

Changed

*create.dotmap: addition of parameters for rectangle border thickness, rectangle border colour.

BoutrosLab.plotting.general 5.6.21

Fixed

• create.scatterplot: adding conditional for when pch is not referring to a point (this is in reference to KM plots)

BoutrosLab.plotting.general 5.6.20

Changed

• create.scatterplot: addition of parameter "col.border". This allows customizable border colours when pch >= 21.

BoutrosLab.plotting.general 5.6.19

Changed

• Pcawg.colours: add project.code to colour.schemes

BoutrosLab.plotting.general 5.6.18

Changed

• create.polygonplot: option to add rectangles.

BoutrosLab.plotting.general 5.6.17

Changed

• Pcawg.colours: consistent colour palette for use on pcawg data

BoutrosLab.plotting.general 5.6.15

Changed

• create.heatmap: rotation of the top x axis labels is now independent from the bottom x axsis labels.
• create.multiplot: options to set the distance between tick marks and tick labels

BoutrosLab.plotting.general 5.6.14

Changed

• create.polygonplot: option to add text.

BoutrosLab.plotting.general 5.6.13

Changed

• create.polygonplot: added parameters alpha and median.lwd.

BoutrosLab.plotting.general 5.6.12

Changed

• create.densityplot & create.violinplot: allow adjustment of bandwidth with parameters bandwidth and bandwidth.adjust.

BoutrosLab.plotting.general 5.6.11

Changed

• create.stripplot: allow different border colour for added points when pch >= 21

BoutrosLab.plotting.general 5.6.10

Fixed

• Reintegrated untagged changes to trunk and re-added scatterplot ## Changed

BoutrosLab.plotting.general 5.6.9

Changed

• create.scatterplot: allow different border colour for added points when pch >= 21

BoutrosLab.plotting.general 5.6.8

Changed

• create.dotmap: Added parameters 'columns' and 'rows' for spot.colour.function to allow dots colours to be grouped by columns or rows, respectively [BPG-16]. There are 12 distinct colours (the default colours) and the colours start to repeat when there are more than 12 columns/rows. It also checks that the columns/rows (depending on which side is selected) are unique and throws and error if they are not.

BoutrosLab.plotting.general 5.6.7

Fixed

• create.multiplot: fixed ## Fixed where NULL values in parameter list (for xlimits=/ylimits=) were being ignored/unprocessed [BPG-2].

BoutrosLab.plotting.general 5.6.6

Changed

• create.barplot: Added parameters 'add.text', 'text.x', 'text.y', 'text.labels', 'text.col', 'text.cex', 'text.fontface' to allow users to add text labels to plot area. Added parameter 'box.ratio' for adjusting thickness of each bar. Added parameter 'remove.all.border.lines' to allow barplots with no borders. Added example for adding text to plot and adjusting box.ratio.

Fixed

• create.barplot: fixed adding error bars for data-frames [BPG-4]

BoutrosLab.plotting.general 5.6.5

Changed

• create.boxplot: Added example for adding text to plot.
• create.hexbinplot: Added example of stratified multiplot.

BoutrosLab.plotting.general 5.6.4

Changed

• create.dotmap: NA plotting character can be made different colours with new variable, NA.spot.size.colour. Default is set to black.

BoutrosLab.plotting.general 5.6.2

Changed

• Get.cor.key: parameterizing number of decimal places to keep for spearman, pearson and kendall correlation values

BoutrosLab.plotting.general 5.4.3

Fixed

• Inconsitency in dotmap/heatmap grid lines location fixed -> everything follows heatmaps spec now fixed ## Fixed where sample.order would reorde barplots incorrectly when horizontal
• Default font sizes are consistent now
• Default font sizes are more proportional

Changed

• Ability to add multiple violin fill colours
• Able to completely remove borders from heatmaps
• Add p values automatically to box plots
• Ability to set a sperate set of defaults based on type of publication ( default sets still need to be added)
• Ability to pick what plots to retrieve plot labels from in create.multiplot

BoutrosLab.plotting.general 5.4.2

Changed

• create.scatterplot: added option to specify colour of grid lines.

BoutrosLab.plotting.general 5.3.9

Changed

• create.heatmap: turns off grid lines when row or column number exceeds a certain threshold.
• Auto-removal of grid lines can be overrided with forcing parameters

BoutrosLab.plotting.general 5.3.7

Fixed

• Same.as.matrix will now correcting readjust label specifications
• When combining scatterplots, they will no longer only use error bars from one scatter plot
• Yaxis.covariates parameter can now allow specific location specification so it does not overlap the heatmap
• Xgrid.at and ygrid.at now properly ## Changed for all functions
• Background rectangles are now drawn in the background instead of foreground
• When combining scatterplots, they will no longer only use the text specified from one scatter plot
• Removed circular definitions from Rd files
• Standardized parameter defaults

Changed

• Can now add subtitles through use of xaxis.top parameters
• Can now input a vector of files to be output to
• Can now sort boxes in create.boxplot by max, min, mean and median (defaults to median if not set)
• Can now draw both bands and lines on segplots
• Polygon plot will now auto-calculate x and y limits if not specified
• Can now vertically align labels and adjust there coordinates manually

BoutrosLab.plotting.general 5.3.4

Changed

• create.scatterplot: ## Changedd ROC example to use auto-label placement

BoutrosLab.plotting.general 5.3.3

Changed

• Functions containing the word 'colour' now accept both American and Canadian spelling

BoutrosLab.plotting.general 5.3.2

Fixed

• create.heatmap: fixed ## Fixed which made labels disappear when stratifying dendrogram

BoutrosLab.plotting.general 5.3.1

Changed

• Minor Updates to the plotting guide

BoutrosLab.plotting.general 5.3.0

Changed

• Standardized parameter names across all plotting functions
• create.hexbinplot: added add.xyline and add.curves functionality (same as in create.scatterplot)

BoutrosLab.plotting.general 5.2.20

Changed

• create.barplot, create.boxplot, create.hexbinplot, create.manhattanplot, create.polygonplot, create.scatterplot, create.segplot, create.stripplot, create.violinplot: Set xlab.label and ylab.label to default to formula components
• Default.colours: greyscale check no longer runs if only one colour is requested

BoutrosLab.plotting.general 5.2.19

Changed

• Force.colour.scheme: added snv colour scheme

BoutrosLab.plotting.general 5.2.18

Changed

• Standardized all plotting functions to have resolution set to 1600 dpi
• Force.colour.scheme: Added spaces in appropriate tissue names

BoutrosLab.plotting.general 5.2.17

Changed

• Removed out-of-date comments from examples

BoutrosLab.plotting.general 5.2.16

Changed

• Re-created PlottingGuide to use revamped show.available.palettes function

BoutrosLab.plotting.general 5.2.13

Changed

• create.multiplot: added example showing how to save parameter options from individual plots

BoutrosLab.plotting.general 5.2.12

Changed

• create.heatmap: Added two parameters: text.position and text.offset to customize placement of text in cells
• Show.available.palettes: changed display of specific schemes to call create.heatmap (more robust method)

BoutrosLab.plotting.general 5.2.10

Fixed

• Show.available.palettes: fixed 'general' program to no longer introduces NAs by coersion

BoutrosLab.plotting.general 5.2.9

Changed

• create.hexbinplot: added comment to explain maxcnt removing datapoints from example plot

BoutrosLab.plotting.general 5.2.8

Changed

• create.barplot: allow vector of custom sorting order for samples
• create.multiplot: has flag to remove all border lines from plots

BoutrosLab.plotting.general 5.2.6

Changed

• Write.plot: fixed ## Fixed
• Added new colourkey legend and interface

BoutrosLab.plotting.general 5.2.5

Changed

• Updated plotting guide to have more examples and slight wording adjustments

BoutrosLab.plotting.general 5.2.4

Changed

• create.barplot: ablines now appear in the background of the plot instead of the foreground

BoutrosLab.plotting.general 5.2.2

Changed

• Write.plot: Added embed.plot functionality (depreciating said function)
• Embed.plot: ## Removed embed.plot()

BoutrosLab.plotting.general 5.2.1

Changed

• Force.colour.scheme: ## Fixed for annovar colour schemes

BoutrosLab.plotting.general 5.2.0

Changed

• Added `Nature' style option to all plotting functions

BoutrosLab.plotting.general 5.1.9

Changed

• create.scatterplot: for add.line.segments, changed line-end style to 'butt'
• create.stripplot: NEW ARGUMENTS to allow for addition of lines showing group medians

BoutrosLab.plotting.general 5.1.7

Changed

• Default.colours: added new schemes spiral.noon and spiral.night
• Default.colours: rearranged order of qual scheme to decrease red-green combinations
• Force.colour.scheme: changed CNV colours to red/blue/green/white, MSI to green/yellow, risk to red/yellow
• Reorganized default.colours and force.colour.scheme to return deprecated schemes
• Show.available.palettes: reorganized layout of 'specific' scheme output

BoutrosLab.plotting.general 5.1.6

Changed

• create.boxplot: added arguments to allow for addition of stripplot in background

BoutrosLab.plotting.general 5.1.5

Changed

• Show.available.palettes: added new function to show schemes available in default.colours and force.colour.scheme
• Default.colours: refactored, changed greyscale warning to auto-calculate

BoutrosLab.plotting.general 5.1.4

Changed

• create.scatterplot: changed argument name - add.lines > add.line.segments
• create.scatterplot: ## Changedd to accept lists of line segments to add

BoutrosLab.plotting.general 5.1.3

Changed

• PlottingGuide: converting to use knitr, added further details and references to design portion
• MultiPlotTutorial: deleted, contents migrated to PlottingGuide

BoutrosLab.plotting.general 5.1.2

Changed

• create.manhattanplot: ## Changedd documentation to use chromosome palette in force.colour.scheme

BoutrosLab.plotting.general 5.1.1

Changed

• create.barplot: changed default fill colour to black (instead of grey)

BoutrosLab.plotting.general 5.1.0

Changed

• create.scatterplot: NEW ARGUMENTS text.guess.* now allows users to specify data points so that associated label positions can be automatically determined
• Inside.rectangle: NEW FUNCTION which determines if a set of data points are inside a set of defined rectangles
• Inside.ellipse: NEW FUNCTION which determines if a set of data points are inside a set of defined ellipses

BoutrosLab.plotting.general 5.0.28

Changed

• Updated plotting guide to have extended design advice: added sections on resolution, file types, etc

BoutrosLab.plotting.general 5.0.27

Changed

• Updated examples in scatterplot, qqplot comparison, hexbinplot, heatmap, dotmap, and barplot to have better formatted axes labels

BoutrosLab.plotting.general 5.0.26

Fixed

• Re-added argument line.lwd in create.scatterplot

BoutrosLab.plotting.general 5.0.25

Changed

• create.heatmap: NEW ARGUMENT gridline.order now allows user to specify in which order gridlines should be drawn (horizontal or vertical first)

BoutrosLab.plotting.general 5.0.24

Changed

• Adjusted examples in qqplot.comparison, qqplot.fit and scatterplot to use character values for panel groupings

BoutrosLab.plotting.general 5.0.23

Changed

• Display.colours now additionally displays names of colours

Fixed

• Added 'eye' to the 'tissue' palette in force.colour.scheme

BoutrosLab.plotting.general 5.0.22

Changed

• Fixed: create.scatterplot, add.lines now works with lists of data

BoutrosLab.plotting.general 5.0.20

Changed

• Changed multiplot example to use matching gene data

BoutrosLab.plotting.general 5.0.19

Changed

• Changing chromosome palette in force.colour.scheme to use more visually distinct colours

BoutrosLab.plotting.general 5.0.18

Fixed

• Changed datasets keep common genes among datasets

BoutrosLab.plotting.general 5.0.17

Changed

• Updated multiplot tutorial with new examples using generate data

BoutrosLab.plotting.general 5.0.16

Fixed

• Default.colours: properly return the requested number of colours when multiple palettes requested

BoutrosLab.plotting.general 5.0.15

Changed

• create.scatterplot:
  • NEW ARGUMENTs allow for addition of line segments to be drawn

Fixed

• Get.corr.key: fixed corner definition determined by x.pos and y.pos

BoutrosLab.plotting.general 5.0.14

Changed

• create.scatterplot:
  • NEW ARGUMENT allows for specification of strip title fontface
• create.stripplot:
  • NEW ARGUMENT allows for specification of strip title fontface

BoutrosLab.plotting.general 5.0.11

Changed

• Added example to create.dotmap clustered by dots and dendrogram added

BoutrosLab.plotting.general 5.0.10

Changed

• Renamed colour schemes in default.colours to follow spiral. format

Changed

• Added biomolecule colour scheme to force.colour.schemes
• Migrated chromosome colour scheme to force.colour scheme from default.colours
• Renamed extra colour schemes in default.colours

BoutrosLab.plotting.general 5.0.9

Changed

• Formatting adjustments to examples

BoutrosLab.plotting.general 5.0.8

Changed

• Changed SNV dataset numerical coding to be simpler

BoutrosLab.plotting.general 5.0.7

Fixed

• Palettes in default.colours function properly return subsets

BoutrosLab.plotting.general 5.0.6

Changed

• Force.colour.scheme now accepts both upper and lower case input

BoutrosLab.plotting.general 5.0.5

Changed

• Changed default sequential, diverging, and binary schemes

BoutrosLab.plotting.general 5.0.4

Changed

• Added more schemes to default.colours

BoutrosLab.plotting.general 5.0.3

Changed

• Added plotting guide to vignettes

BoutrosLab.plotting.general 5.0.2

Fixed

• create.barplot:
  • Re-added origin to panel call to allow for negative bars
  • Set y-axis default values to appear automatically
  • Fixed ordering of bars by increasing data
• create.histogram: Silenced warning caused by data parameter

BoutrosLab.plotting.general 5.0.1

Changed

• Force.colour.scheme: Added colour schemes in addition to the 'annovar' schemes
• Default.colours: Added additional 5-colour palette

BoutrosLab.plotting.general 5.0.0

Added

• create.scatterplot.with.error: ## Removed function, merged with create.scatterplot
• Panel.BL.bwplot: ## Removed function, functionality no longer needed
• create.multiple.stripplots: ## Removed function, functionality contained within create.stripplot
• create.multiple.boxplots: ## Removed function, functionality contained within create.boxplot
• create.barplot.with.error: ## Removed function, functionality contained within create.barplot
• Rgb.to.greyscale: ## Removed function, moved into display.colours
• Colour.to.grey: ## Removed function, moved into display.colours
• Scientific.notation.2: ## Removed function, functionality contained within scientific.notation
• Scientific.notation.expr: ## Removed function, functionality contained within scientific.notation
• create.violinplot: Renamed function from create.violin.plot
• create.polygonplot: Renamed function from create.polygon

Changed

• Code and documentation base reviewed to match lab formatting standard
• Updating examples in documentation to use standard datasets instead of fake data
• create.multiplot: ## Changedd example plots to use standard dataset
• Patient: Added additional data to show proportions of base changes
• create.scatterplot: Added example using error bars
• Scientific.notation: Now returns either an expression or list
• Updated test-suite to save a single multiplot to file

BoutrosLab.plotting.general 4.3.14

Changed

• Updated test suite to remove soon-to-be deleted plotting functions

BoutrosLab.plotting.general 4.3.13

Changed

• Formatted examples in documentation to contain less than 100 characters per line
• SNV: changed encoding of dataset to use numerical values instead of character values

BoutrosLab.plotting.general 4.3.12

Changed

• create.violin.plot: ## Changedd example plots to use standard dataset

BoutrosLab.plotting.general 4.3.11

Changed

• create.stripplot: ## Changedd example plots to use standard dataset

BoutrosLab.plotting.general 4.3.10

Changed

• create.stripplot: Exposing xat and xlimits parameter to allow for customization of horizontal plots

BoutrosLab.plotting.general 4.3.9

Changed

• create.segplot: ## Changedd example plots to use standard dataset

BoutrosLab.plotting.general 4.3.8

Changed

• create.scatterplot: ## Changedd example plots to use standard dataset

BoutrosLab.plotting.general 4.3.7

Changed

• Removed old datasets and ## Changedd documentation examples to use newly formatted data
• Set LazyData in DESCRIPTION to 'yes' so that datasets can be referenced by name alone

BoutrosLab.plotting.general 4.3.6

Changed

• CNA, SNV, microarray, patient: Added new datasets to data/ folder, each with a corresponding Rd file
• Deleted old 'p value' dataset formerly used for create.manhattanplot examples

BoutrosLab.plotting.general 4.3.5

Changed

• create.colourkey: Fixed formatting in documentation to fit under 90 characters per line
• create.histogram: ## Changedd example code to check dataset size instead of use hard-coded values
• Microarray: Decreased size of microarray dataset

BoutrosLab.plotting.general 4.3.4

Changed

• create.colourkey: Exposed parameter for colourkey cex

BoutrosLab.plotting.general 4.3.3

Changed

• create.qqplot.fit: ## Changedd example plots to use standard dataset

BoutrosLab.plotting.general 4.3.2

Changed

• create.qqplot.comparison: ## Changedd example plots to use standard dataset
• MultiPlotTutorial: Reduced file size

BoutrosLab.plotting.general 4.3.1

Changed

• create.polygon: ## Changedd example plots to use standard dataset

BoutrosLab.plotting.general 4.3.0

Changed

• Run_plots: Added test script to package

BoutrosLab.plotting.general 4.2.40

Changed

• create.histogram: ## Changedd example plots to use standard dataset

BoutrosLab.plotting.general 4.2.39

Changed

• create.hexbinplot: ## Changedd example plots to use standard dataset

BoutrosLab.plotting.general 4.2.38

Changed

• create.dotmap: ## Changedd example plots to use standard dataset

BoutrosLab.plotting.general 4.2.37

Changed

• create.densityplot: ## Changedd example plots to use standard dataset

BoutrosLab.plotting.general 4.2.36

Changed

• create.boxplot: ## Changedd example plots to use standard dataset

BoutrosLab.plotting.general 4.2.35

Changed

• create.heatmap: ## Changedd example plots to use standard dataset

BoutrosLab.plotting.general 4.2.34

Fixed

• create.heatmap: Fixed error where heatmap threw error if symbols were added, but not 'border' symbols

BoutrosLab.plotting.general 4.2.33

Changed

• create.heatmap: Added clarification to documentation that 'colour.alpha' can be set to 'automatic'
• create.multiplot: Expose parameters for x-axis and y-axis tick mark lengths

BoutrosLab.plotting.general 4.2.32

Changed

• create.violinplot: ## Removed error message for using pch>=21 with lattice version 20-13
• create.violinplot: Modified handling of border and fill colours for extra points

BoutrosLab.plotting.general 4.2.31

Changed

• create.manhattanplot: ## Changedd example plots to use standard dataset

BoutrosLab.plotting.general 4.2.30

Changed

• create.barplot: ## Changedd example plots to use standard dataset

BoutrosLab.plotting.general 4.2.29

Changed

• create.dotmap: enabled default behaviour for NA values to plot 'X' characters size 7

BoutrosLab.plotting.general 4.2.28

Changed

• create.dotmap: Improved handling of multiple pch with multiple fill colours

BoutrosLab.plotting.general 4.2.27

Changed

• create.dotmap: Deleted warning for using pch>=21 with lattice version 20-13 (outdated)

BoutrosLab.plotting.general 4.2.26

Changed

• create.dotmap: Stopped printing of warning regarding using pch>=21 with lattice version 20-13

BoutrosLab.plotting.general 4.2.25

Changed

• Fixed spelling errors in documentation and code

BoutrosLab.plotting.general 4.2.24

Changed

• Embed.plot: Added example & ## Changedd documentation to use proper parameters
• create.hexbinplot: Fixed formatting issue
• create.scatterplot: Fixed auto-sensing of labels
• create.barplot: Added functionality of adding text above bars
• create.heatmap: Added ability to have multi-sized borders
• create.heatmap: Adjusted input of 'main' to accept non-list values
• MultiPlotTutorial: Compressed pdf
• Updated formatting of all function documentation
• NAMESPACE: Added imports

BoutrosLab.plotting.general 4.2.23

Changed

• create.densityplot: Added data-sensing
• create.scatterplot: Added data-sensing
• create.hexbinplot: Added example of multi-colour scheme

BoutrosLab.plotting.general 4.2.22

Changed

• create.densityplot: Expose top, bottom, left, and right padding parameters
• create.hexbinplot: Expose top, bottom, left, and right padding parameters
• create.qqplot.fit: Expose top, bottom, left, and right padding parameters
• create.qqplot.comparison: Expose top, bottom, left, and right padding parameters
• create.violin.plot: Expose top, bottom, left, and right padding parameters
• create.heatmap: Added removal of top bar in stratified dendrograms

Fixed

• Fixed ## Fixeds, typos, and mismatches in multiplot tutorial sample code
• create.heatmap: Fixed coding issues

BoutrosLab.plotting.general 4.2.21

Changed

• Embed.plot: Added new function to allow for plot-within-a-plot layouts

BoutrosLab.plotting.general 4.2.20

Changed

• create.heatmap: Added ability to automatically estimate values for colour.alpha parameter
• create.heatmap: Added example for automatic colour.alpha value estimation

Fixed

• create.heatmap: Fixed grid to also draw lines on first row & column
• create.barplot: Fixed default units to inches
• create.heatmap: Fixed documentation to match changes in code
• create.boxplot: Fixed naming issue
• create.multiplot: Fixed naming conventions

BoutrosLab.plotting.general 4.2.19

Changed

• Added new function 'colour.gradient' to generate sequential colour palettes

BoutrosLab.plotting.general 4.2.18

Changed

• create.heatmap: Added ability to stratify dendrogram
• create.boxplot: Added ability to reorder boxplots based on median values

BoutrosLab.plotting.general 4.2.17

Changed

• create.barplot: Added ability to draw curves
• create.boxplot: Added ability to draw curves
• create.barplot.with.error: Adjusted whisker length to not cover whole bar
• create.heatmap: Added example of per-cell font characteristics
• create.barplot: Added example of grouped labels
• create.boxplot: Added option of drawing line either in front of or behind plot

Fixed

• create.heatmap: Fixed issue with symbols

BoutrosLab.plotting.general 4.2.16

Changed

• create.heatmap: Added global covariate outline
• create.barplot: Added grouping of labels for grouped barplot
• create.heatmap: Added examples
• create.multiplot: Added examples

Fixed

• Write.metadata: Fixed to stop printing warnings

BoutrosLab.plotting.general 4.2.15

Changed

• create.multiplot: Added ability to retrieve plot labels & limits from 'original' plots
• create.multiplot: ## Changedd examples

Fixed

• Scientific.notation.expr: Fixed issue & code formatting
• Write.metadata: Fixed issue with dependencies

BoutrosLab.plotting.general 4.2.14

Changed

• create.heatmap: Added functionality of inserting additional symbols
• create.heatmap: Added example to documentation of symbol usage
• create.scatterplot: Changed ablines to be drawn in front of plot
• Added datasets files to inst folder for later use in examples
• Added vignettes folder containing multiplot tutorial

Fixed

• create.barplot: Fixing reordering of bars

BoutrosLab.plotting.general 4.2.13

Changed

• create.barplot: Set default reordering to FALSE
• create.dotmap: Added functionality to change dot colour

BoutrosLab.plotting.general 4.2.12

Changed

• create.barplot: Added functionality to reorder bars to be increasing or decreasing
• create.hexbinplot: Added more examples
• Exposed 'fontface' parameter in all plotting functions

BoutrosLab.plotting.general 4.2.11

Changed

• Display.statistical.result: ## Changedd defaults in documentation

BoutrosLab.plotting.general 4.2.10

Changed

• create.hexbinplot: Added background colour
• create.hexbinplot: Added ability to have tick marks on top x axis only
• create.hexbinplot: Enabled svg output
• create.hexbinplot: Added examples to documentation

Fixed

• create.barplot: ## Removed origin from panel call to enable creation of stacked, horizontal, unidirectional plots

BoutrosLab.plotting.general 4.2.9

Changed

• Display.statistical.result: Added option to change ":" to a different symbol
• create.hexbinplot: Added ability to change background colour
• create.heatmap: Added ability to display tick marks on top axis only
• Enabled svg output for all plots

BoutrosLab.plotting.general 4.2.8

Changed

• Re-added package

BoutrosLab.plotting.general 4.2.7

Added

• Added create.manhattanplot function

BoutrosLab.plotting.general 4.2.4

Changed

• Added TODO file

BoutrosLab.plotting.general 4.2.3

Changed

• create.boxplot: Added ability to draw rectangle panels
• create.boxplot: Added new example with grey shading between different boxes

BoutrosLab.plotting.general 4.2.2

Changed

• create.barplot: Added ability to change the width of the box

BoutrosLab.plotting.general 4.2.1

Changed

• create.barplot: Added new parameters - background.col and draw.grid
• create.barplot: Added new example of grey background with white grid lines

BoutrosLab.plotting.general 4.2.0

Changed

• Default.colours: Changed default qualitative palette to have brighter colours, and 12 options instead of only 9. Previous qualitative palette still accessible by setting palette.type = 'old.qual'

BoutrosLab.plotting.general 4.1.8

Changed

• Default.colours: ## Removed deprecated survival colour scheme
• Changed warning about greyscale compatibility to be more general

BoutrosLab.plotting.general 4.1.7

Changed

• Default.colours: ## Removed deprecated old chromosome colour scheme
• Replaced 'sandybrown' with 'tan1' in new chromosome palette

BoutrosLab.plotting.general 4.1.6

Changed

• Added create.colourkey to NAMESPACE

BoutrosLab.plotting.general 4.1.5

Changed

• Update and reorder NAMESPACE

BoutrosLab.plotting.general 4.1.4

Changed

• Removed unnecessary requires in get.corr.key

BoutrosLab.plotting.general 4.1.3

Changed

• Updated minimum required versions of dependencies

BoutrosLab.plotting.general 4.1.2

Changed

• create.barplot: ## Changedd manual to reflect addition of 'axis.fontface' argument
• create.colourkey: ## Removed 'enable.warnings' argument

BoutrosLab.plotting.general 4.1.1

Changed

• create.barplot: Added arguments 'xaxis.fontface' and 'yaxis.fontface'

BoutrosLab.plotting.general 4.1.0

Added

• Added new function: 'create.colourkey' to generate and draw colourkey

BoutrosLab.plotting.general 4.0.7

Changed

• create.stripplot: New arguments 'xaxis.fontface', 'yaxis.fontface' to allow for modification of axis tck label font face
• create.stripplot: New argument 'ylab.axis.padding' allows for modification of padding between yaxis label and tck labels

BoutrosLab.plotting.general 4.0.6

Changed

• create.dendrogram: ## Changedd documentation for jaccard usage
• create.heatmap: ## Changedd documentation for jaccard usage
• create.heatmap: Moved logic for x.tck out of level plot

BoutrosLab.plotting.general 4.0.5

Changed

• create.heatmap: Refactoring and cleanup of code

BoutrosLab.plotting.general 4.0.4

Changed

• create.polygon: Added 'median.lty' (for seq power plot)

BoutrosLab.plotting.general 4.0.3

Changed

• create.hexbinplot: Changed default of 'mincnt' to 1 (from 0)

BoutrosLab.plotting.general 4.0.2

Changed

• create.scatterplot.with.error: New arguments to specify plot layout and placement - 'layout', 'as.table', 'x.spacing', 'y.spacing'
• create.polygon: Added parameters 'axis.log' and 'yaxis.log'

BoutrosLab.plotting.general 4.0.1

Changed

• create.dotmap: Added example

BoutrosLab.plotting.general 4.0.0

Added

• Added 'write.metadata' function
• Added 'description' parameter to all plotting function documentations
• Write.metadata: Added 'operating system', 'machine', 'system2'
• create.multiplot: ## Changedd documentation

BoutrosLab.plotting.general 3.10.2

Changed

• Default.colours: ## Changed chromosome colour scheme to be coded by letter-names rather than numbers, and using more easily-distinguished colours

BoutrosLab.plotting.general 3.10.1

Changed

• Legend.grob: Added ability to specify size (width) of legend boxes for each legend individually

BoutrosLab.plotting.general 3.10.0

Added

• create.scatterplot: Added parameter 'axis.key.padding' to adjust spacing between y-axis and key
• create.scatterplot: Added parameters 'add.points', 'points.x', 'points.y', 'points.col', 'points.pch', 'points.cex' - allow users to add additional points to plot area
• create.scatterplot: Added parameters 'add.text', 'text.x', 'text.y', 'text.labels', 'text.col', 'text.cex', 'text.fontface' - allow users to add text labels to plot area

BoutrosLab.plotting.general 3.9.6

Changed

• create.dotmap: Added padding parameter

BoutrosLab.plotting.general 3.9.5

Changed

• create.barplot: Adjustments to spacing and commenting
• create.dotmap: Added ability to specify padding on all sides of plot

BoutrosLab.plotting.general 3.9.4

Changed

• create.multiplot: New argument 'axes.lwd' to specify border line thickness

BoutrosLab.plotting.general 3.9.3

Changed

• create.multiplot: Fixed 'xlab.to.xaxis.padding' variable to change the correct parameter

BoutrosLab.plotting.general 3.9.2

Changed

• create.heatmap: Added ability to specify two x-axes, and gave meaning to 'x-alternating = 3' (prints tick marks on top and bottom x axes)
• create.multiplot: Added 'xlab.to.xaxis.padding' parameter

BoutrosLab.plotting.general 3.9.1

Changed

• create.dotmap: Replaced 'grid.colour' with 'row.colour' and 'col.colour'
• create.barplot: ## Changedd to accept arguments that handle background shading
• create.heatmap: Added 'xaxis.tck' and 'yaxis.tck' parameters to override default values based on covariate size

BoutrosLab.plotting.general 3.9.0

Changed

• create.multiplot: Added 'layout.skip' parameter to allow for blank spots in layout, and also added a complex example

BoutrosLab.plotting.general 3.8.7

Changed

• Rgb.to.greyscale: Changing function to return results, rather than print

BoutrosLab.plotting.general 3.8.6

Changed

• Append.footnote: Added function to create plot footnotes
• Default.colours: Fixed method of returning one-colour palettes for backwards compatibility

BoutrosLab.plotting.general 3.8.5

Changed

• Default.colours: Adjustments to chromosome colour palette
• Default.colours: Added ability to provide multiple sequential and binary colour schemes

BoutrosLab.plotting.general 3.8.4

Changed

• create.boxplot: Added ability to define 'abline.v'

BoutrosLab.plotting.general 3.8.3

Changed

• Display.colours: Added function to view colour palettes and what they look like in grey scale

BoutrosLab.plotting.general 3.8.2

Changed

• Covariates.grob: Added 'reorder.grid.index' parameter to specify ordering of grid indices
• create.heatmap: Added 'covariates.reorder.grid.index' and 'covariates.top.reorder.grid.index' parameters to match changes to covariates.grob

BoutrosLab.plotting.general 3.8.1

Changed

• create.heatmap: Split 'grid.colour' and 'grid.lwd' parameters into 'row.colour/col.colour' and 'row.lwd/col.lwd'
• create.heatmap: Added grandfather parameters for 'grid.colour' and 'grid.lwd'

BoutrosLab.plotting.general 3.8.0

Added

• Colour.to.grey: Added new function to convert R colours to R grey colours

BoutrosLab.plotting.general 3.7.0

Added

• create.heatmap: Added 'covariates.row.lines', 'covariates.col.lines', 'covariates.top.row.lines', 'covariates.top.col.lines' corresponding to new covariates.grob arguments, and ## Changedd examples
• Covariates.grob: Added parameters 'row.lines' and 'col.lines' to allow user to specify which grid lines to draw in covariate bars, and ## Changedd examples

BoutrosLab.plotting.general 3.6.20

Changed

• Get.corr.key: New arguments to allow for the addition of a title to the key

BoutrosLab.plotting.general 3.6.19

Changed

• create.barplot: Attempting to make sizes match up
• create.dotmap: Can now have custom colours specified
• Write.plot: Code formatting changes

BoutrosLab.plotting.general 3.6.18

Changed

• create.barplot: Code clean-up to match coding standards

BoutrosLab.plotting.general 3.6.17

Changed

• create.barplot: Fix to align error bars when barplot is grouped
• Write.plot: Refactor to place extension-specific code in inst/ext2function.txt

BoutrosLab.plotting.general 3.6.16

Changed

• Write.plot: Allowing pdf and png output

BoutrosLab.plotting.general 3.6.15

Changed

• create.segplot: Added 'abline.h' parameter

BoutrosLab.plotting.general 3.6.14

Changed

• create.heatmap: Centralize parameter-checking code at start of script
• Added pch>=21 warning to appropriate R files, and ## Removed ^M

BoutrosLab.plotting.general 3.6.13

Changed

• create.polygon: Added line plotting options 'add.xyline', 'abline.h', 'abline.v'
• create.barplot: Added examples

BoutrosLab.plotting.general 3.6.12

Changed

• create.multiplot: Added check for NAs in the legends workaround

BoutrosLab.plotting.general 3.6.11

Changed

• create.multiplot: Added workaround for lattice being unable to accept multiple legends with the same name via ## Changed.trellis
• create.multiplot: Allowed x/y-relations between plots to be set

BoutrosLab.plotting.general 3.6.10

Changed

• create.multiplot: Added 'xlab.padding', and 'key.bottom.padding'
• Added copyright header to R files

BoutrosLab.plotting.general 3.6.9

Changed

• create.barplot: Updating with "raster" command
• create.multiplot: Making examples prettier, moving key.bottom.padding into argument

BoutrosLab.plotting.general 3.6.8

Changed

• create.barplot: Merging with create.barplot.with.error
• create.barplot.with.error: Merging with create.barplot
• Create multiplot: Adding 'xaxis.fontface', 'yaxis.fontface' to allow for specification of axis-label fontface

BoutrosLab.plotting.general 3.6.7

Changed

• create.scatterplot: Added explicit horizontal argument
• create.barplot: Added options to specify distance between x-axis and label
• create.scatterplot: Add options to pass arbitrary plots onto lattice:xyplot
• create.barplot.with.error: Fixing documentation
• create.barplot: Allow user to edit 'key.bottom'
• create.stripplot: Added parameters to allow for different border/fill colours (for pch 21:25), 'colour.alpha' to allow for plotting character transparencies, 'as.table', 'x.spacing', 'y.spacing' for customization of panels

BoutrosLab.plotting.general 3.6.6

Changed

• create.dotmap: Added argument 'pch.border.col' to set colour of dot border if pch is 21:25

BoutrosLab.plotting.general 3.6.5

Changed

• create.scatterplot: Added 'key.left.padding' parameter to place legends to left of graph
• create.scatterplot: Added 'axes.lty' to set line style of axes lines
• Force.colour.scheme: Added another colour palette
• create.multiplot: Added three parameters - 'xaxis.rot', 'key.left.padding', 'key.right.padding'

BoutrosLab.plotting.general 3.6.4

Changed

• create.heatmap: Added option of including x and y axis label covariates (between label and heatmap), and examples

BoutrosLab.plotting.general 3.6.3

Changed

• Force.colour.scheme: Added alternative colour scheme for annovar output

BoutrosLab.plotting.general 3.6.2

Changed

• Get.corr.key: Added missing else case for beta1.p
• Force.colour.scheme: Added synonymous SNV to the list

BoutrosLab.plotting.general 3.6.1

Changed

• create.multiplot: Changed key.left value to 1 so that legends can be placed to left of multiplot area

BoutrosLab.plotting.general 3.6.0

Added

• create.scatterplot: Added ability to draw rectangles in background

BoutrosLab.plotting.general 3.5.17

Changed

• create.polygon: Changed default values of 'xgrid.at' and 'ygrid.at'
• create.polygon: Added 'xaxis.fontface' and 'yaxis.fontface'
• create.polygon: Added 'fontface = xaxis.fontface' and 'fontface = yaxis.fontface' to scales$x and scales$y
• create.polygon: Added example to demonstrate use with legend.grob

BoutrosLab.plotting.general 3.5.16

Changed

• create.polygon: Adjusted values of par.settings$layout.widths$axis.key.padding and par.settings$layout.heights$axis.key.padding to equal 1 - this lets the legend on the right be properly rendered

BoutrosLab.plotting.general 3.5.15

Changed

• create.barplot: Added ability to create horizontal barplots - 'plot.horizontal', 'xlimits', and 'xat' parameters added & example

BoutrosLab.plotting.general 3.5.14

Changed

• create.scatterplot: Fixing example to adjust placement of yaxis title
• create.dotmap: Adding parameter 'fill.colour' to allow user to fill background of cells

BoutrosLab.plotting.general 3.5.13

Changed

• Force.colour.scheme: Added overload functionality, changed scheme
• Updating date with version

BoutrosLab.plotting.general 3.5.12

Changed

• Force.colour.scheme: Added new force colour scheme function

Changed

• create.barplot: Added ability to draw vertical lines

BoutrosLab.plotting.general 3.5.11

Changed

• create.multiplot: ## Changedd documentation to show to remove tick marks

BoutrosLab.plotting.general 3.5.10

Changed

• Get.line.breaks: Added get line breaks function

BoutrosLab.plotting.general 3.5.9

Changed

• create.heatmap: Added check for ## Changed

BoutrosLab.plotting.general 3.5.8

Changed

• create.polygon: Reverted functionality back to using if statements instead of ternary operators
• create.heatmap: Added covariate bar between heatmap and xaxis labels

BoutrosLab.plotting.general 3.5.7

Changed

• create.dotmap: Added 'grid.col.lwd' and 'grid.row.lwd' to allow different weights of gridlines

BoutrosLab.plotting.general 3.5.6

Changed

• create.dotmap: ## Changedd 'key.left', 'key.right', 'key.bottom' to default to 1 so that legends/keys are properly incorporated
• create.dotmap: Added example using covariate bar and legend

BoutrosLab.plotting.general 3.5.5

Changed

• create.heatmap: Use grobPack() fontfamily specification to avoid unknown Arial font specification
• create.dotmap: Changed yaxis label default to not be bold
• Legend.grob: Added parameters - 'layout', 'between.col', 'between.row' to allow user to specify layout for multiple legends and set empty space between rows/columns
• Legend.grob: Changed titles in legend to use a text grob instead of draw.key
• create.heatmap: Added 'legend.layout', 'legend.between.col', and 'legend.between.row' parameters

BoutrosLab.plotting.general 3.5.4

Changed

• create.dotmap: ## Changedd to use dotmap colour scheme by default, fixed palette creation for >3 colour schemes
• create.dotmap: Added example with 5-colour background

BoutrosLab.plotting.general 3.5.3

Changed

• create.heatmap: Added set.seed() call at beginning of examples

BoutrosLab.plotting.general 3.5.2

Changed

• create.scatterplot: Fixed codoc error
• General fixes for coding-style standardization and document fixes
• Updates to dependency versions

BoutrosLab.plotting.general 3.5.1

Changed

• create.scatterplot: Changed default curves to use min/max with na.rm=T

BoutrosLab.plotting.general 3.5.0

Added

• Covariates.grob: Added parameters 'grid.row', 'grid.col', 'grid.border' to allow customization of grid lines within covariate bars
• create.heatmap: Added parameters 'covariates.grid.row', 'covariates.grid.col', 'covariates.grid.border', 'covariates.top.grid.row', 'covariates.top.grid.col', 'covariates.top.grid.border', 'legend.border', 'legend.border.padding'
• create.heatmap: Added parameters 'covariates.padding', and 'covariates.top.padding' to allow for empty space between covariate bars and dendrograms
• Legend.grob: Added parameters 'border', 'border.padding' to allow for border around legend
• Updated examples

BoutrosLab.plotting.general 3.4.4

Changed

• Display.statistical.result: Added space before and after "x" sign

BoutrosLab.plotting.general 3.4.3

Changed

• create.heatmap: Changed 'grid.row' and 'grid.col' to default to false
• create.heatmap: No longer assumes that matrices with less than 125 rows/columns should have grid lines

BoutrosLab.plotting.general 3.4.2

Changed

• Display.statistical.result: Migrating this function to plotting.general

BoutrosLab.plotting.general 3.4.1

Changed

• create.heatmap: Added code to close devices opened by the grid::covertUnit function and remove Rplots.pdf files if necessary
• Legend.grob: Added code to remove Rplots.pdf files created by the lattice::draw.key

BoutrosLab.plotting.general 3.4.0

Added

• Default.colours: Added gender colour palette
• create.dendrogram: Interface change - renamed cluster.dimensions (pl.) to cluster.dimension (s.) because only takes scalars
• create.dendrogram: Code clean-up
• create.dendrogram: Fixed handling of jaccard distance

BoutrosLab.plotting.general 3.3.7

Changed

• create.segplot: ## Removed warning caused by typo in man file

BoutrosLab.plotting.general 3.3.6

Changed

• Legend.grob: Added code to close extra device created by the draw.key()

BoutrosLab.plotting.general 3.3.5

Changed

• create.densityplot: Set groups to an ordered factor (avoids auto-alphabetical ordering by lattice during plotting)

BoutrosLab.plotting.general 3.3.4

Changed

• create.polygon: Added example

BoutrosLab.plotting.general 3.3.3

Changed

• create.segplot: ## Removed unused parameter from function definition & fixed inconsistencies

BoutrosLab.plotting.general 3.3.2

Changed

• create.boxplot: Replaced call to panel.BL.bwplot with call to panel.bwplot

BoutrosLab.plotting.general 3.3.1

Changed

• Default.colours: Added new 2-colour scheme for dotmaps
• create.dotmap: ## Changedd example to use new dotmap colour scheme from default.colours

BoutrosLab.plotting.general 3.3.0

Changed

• create.segplot: Added new function to create segplots

BoutrosLab.plotting.general 3.2.31

Changed

• create.heatmap: Added notes in help file for using euclidean when lots of ties and correlation fails
• Legend.grob: Added notes in help file for using euclidean when lots of ties and correlation fails

BoutrosLab.plotting.general 3.2.30

Changed

• create.violinplot: Fixed a ## Fixed in extra points argument
• create.scatterplot: Added alpha argument to control plotting transparency

BoutrosLab.plotting.general 3.2.29

Changed

• create.dendrogram: ## Changedd to use dist(method = "jaccard") instead of jaccard.distance()

BoutrosLab.plotting.general 3.2.28

Changed

• Default.colours: Changed warning message when survival colour scheme is used with more than 5 colours

BoutrosLab.plotting.general 3.2.27

Changed

• create.polygon: Fixed border.col argument to allow different coloured borders for multiple groups

BoutrosLab.plotting.general 3.2.26

Changed

• create.dendrogram: Changed jaccard.distance to use 't(x)' instead of 'x' in order to imitate behaviour of dist function

BoutrosLab.plotting.general 3.2.25

Changed

• create.polygon: New arguments 'extra.points', 'extra.points.cex', 'extra.points.col', to allow for points plotted on top of main plot
• create.polygon: New arguments 'xgrid.at', 'ygrid.at', 'grid.col' to allow for grid lines in the background of the main plot
• create.violin.plot: New arguments 'extra.points', 'extra.points.cex', 'extra.points.col', to allow for points plotted on top of main plot
• create.violin.plot: New arguments 'fill.colour', 'border.lwd' to allow for control of interior colours and exterior border widths

BoutrosLab.plotting.general 3.2.24

Changed

• create.scatterplot.with.error: New arguments 'strip.col', 'strip.cex' to control size and background colour of panel labels
• create.scatterplot.with.error: New argument 'error.bar.length' to adjust size of error bar whiskers

BoutrosLab.plotting.general 3.2.23

Changed

• create.stripplot: Added parameters for groups, layout, padding around graph, key and legend, and example for how to use 'groups' parameter

BoutrosLab.plotting.general 3.2.22

Changed

• Default.colours: Changed greyscale warning message for survival palette

BoutrosLab.plotting.general 3.2.21

Changed

• create.barplot: Added example using covariates with labels/covariate legend
• create.scatterplot: Added example using covariates with labels/covariate legend

BoutrosLab.plotting.general 3.2.20

Changed

• create.heatmap: Resolved codoc mismatch introduced in v3.2.19
• Updated package dependencies to newer versions

BoutrosLab.plotting.general 3.2.19

Changed

• create.heatmap: Replaced arguments 'border' and 'border.lwd' with 'grid.colour' and 'grid.lwd'
• create.heatmap: Added ability to turn off interior gridlines using 'grid.row=FALSE', 'grid.col=FALSE' or 'grid.lwd=0'

BoutrosLab.plotting.general 3.2.18

Changed

• create.dendrogram: ## Changedd to use jaccard.distance instead of vegdist
• Removed vegan dependency from DESCRIPTION

BoutrosLab.plotting.general 3.2.17

Changed

• Panel.BL.bwplot: Changed 'nr' to 'nrow' in matrix call to avoid check warnings
• Default.colours: Changed colours in survival palette

BoutrosLab.plotting.general 3.2.16

Changed

• Get.corr.key: Added robust regression coefficients and example using outlier
• Added dependency on package MASS

BoutrosLab.plotting.general 3.2.15

Changed

• Changing vegan dependency version to be lower
• Default.colours: Added survival palette and explanation in file as to how to add a new palette

BoutrosLab.plotting.general 3.2.14

Changed

• Default.colours: Code clean-up and added ability to use chromosome colour scheme

BoutrosLab.plotting.general 3.2.13

Changed

• Get.corr.key: Changed default resolution in create.survival.plot from 2000 to 100
• create.histogram: Added support for horizontal and vertical abline

BoutrosLab.plotting.general 3.2.12

Changed

• Default.colours: Fixed return value for Venn diagram palettes to return a list of both fill colours and text colours, as per example in documentation

BoutrosLab.plotting.general 3.2.11

Changed

• create.heatmap: Added 'text.col' parameter
• create.heatmap: Added example of using unicode symbols instead of text - similar to dotmap, but allows clustering

BoutrosLab.plotting.general 3.2.10

Changed

• create.heatmap: Correct ordering of text in clustered data

BoutrosLab.plotting.general 3.2.9

Changed

• create.scatterplot: Reordered 'legend' and 'layout.width' arguments to fix padding issues
• create.scatterplot.with.error: Reordered 'legend' and 'layout.width' arguments to fix padding issues

BoutrosLab.plotting.general 3.2.8

Changed

• create.stripplot: Added 'jitter' argument to allow for staggering of data along x-axis

BoutrosLab.plotting.general 3.2.7

Changed

• create.histogram: Added parameters for padding, spacing, layout, panel
• create.histogram: Specifying type = "cairo" for all tiff() calls in Rd files - needed for building package on Mac
• Covariates.grob: Specifying type = "cairo" for all tiff() calls in Rd files - needed for building package on Mac
• create.multiplot: Specifying type = "cairo" for all tiff() calls in Rd files - needed for building package on Mac
• Legend.grob: Specifying type = "cairo" for all tiff() calls in Rd files - needed for building package on Mac

BoutrosLab.plotting.general 3.2.6

Changed

• create.scatterplot: Added option 'abline.v' to draw vertical lines

BoutrosLab.plotting.general 3.2.5

Changed

• create.densityplot: Fixed ## Fixed when grids are added - now if type=c("g","l"), xyplot.panels do not double call "g" circle symbols instead of lines
• create.multiple.boxplots: ## Changedd x-axis label/rotation variable names to match other plotting functions & added argument to allow for specification of main.cex
• create.stripplot: ## Changedd x-axis rotation variable name to match other plotting functions & added arguments to specify x/ylab.col, x/yaxis.col/tck/rot
• create.violinplot: ## Changedd x-axis label/rotation variable names to match other plotting functions & added arguments to allow for specification of x/ylab.col, x/yaxis.col/tck/rot

BoutrosLab.plotting.general 3.2.4

Changed

• create.histogram: Added arguments to allow for specification of x/yaxis.col/tck, x/ylab.col, x/yaxis.rot
• create.polygon: Added arguments to allow for specification of x/yaxis.col/tck, x/ylab.col, x/yaxis.rot
• create.qqplot.comparison: Added arguments to allow for specification of x/yaxis.col/tck, x/ylab.col
• create.qqplot.fit: Added arguments to allow for specification of x/yaxis.col/tck, x/ylab.col
• create.scatterplot: Added arguments to allow for specification of x/yaxis.col/tck, x/ylab.col
• create.scatterplot.with.error: Added arguments to allow for specification of x/yaxis.col/tck, x/ylab.col

BoutrosLab.plotting.general 3.2.3

Changed

• create.barplot: Added example with covariates

BoutrosLab.plotting.general 3.2.2

Changed

• create.multiplot: Adjusted formatting and ## Removed de## Fixedging code
• create.scatterplot: Added option 'abline.v' to draw vertical lines
• create.heatmap: ## Changedd x/y label variable names to match other plotting functions, and added arguments to allow for specification of 'yaxis.rot', 'xaxis.col', 'yaxis.col', 'xlab.col', 'ylab.col', 'main.cex
• create.hexbinplot: ## Changedd x/y label variable names to match other plotting functions, and added arguments to allow for specification of 'yaxis.rot', 'xaxis.col', 'yaxis.col', 'xlab.col', 'ylab.col', 'xaxis.tck', 'yaxis.tck'
• create.dotmap: ## Changedd x/y label and x/y cex variable names to match other plotting functions, and added arguments to allow for specification of 'yaxis.rot', 'xaxis.col', 'yaxis.col', 'xlab.col', 'ylab.col'

BoutrosLab.plotting.general 3.2.1

Changed

• create.multiplot: Clarified labels on 6 panel example
• create.barplot: ## Changedd examples to use new variables
• create.densityplot: ## Changedd examples to include new variables

BoutrosLab.plotting.general 3.2.0

Added

• create.multiplot: Added example with 6 panels & modified variable names to be consistent
• create.barplot: Changed x/yaxis label variable names, ## Changedd to accept arguments for x/yaxis rotation, x/y axis label and tick label colour, and length of x/y axis tick marks
• create.barplot.with.error: Changed x/yaxis label variable names, ## Changedd to accept arguments for x/yaxis rotation, x/y axis label and tick label colour, and length of x/y axis tick marks
• create.boxplot: Changed x/yaxis label variable names, ## Changedd to accept arguments for x/yaxis rotation, x/y axis label and tick label colour, and length of x/y axis tick marks
• create.densityplot: Changed x/yaxis label variable names, ## Changedd to accept arguments for x/yaxis rotation, x/y axis label and tick label colour, and length of x/y axis tick marks

BoutrosLab.plotting.general 3.1.16

Changed

• create.stripplot: Implemented customizable character colour
• create.multiple.stripplots: Implemented customizable character colour

BoutrosLab.plotting.general 3.1.15

Changed

• create.multiplot: Improved consistency of test output file names and variable names
• create.densityplot: Changed defaults to not display axis lines
• create.hexbinplot: Changed defaults to not display axis lines
• create.scatterplot.with.error: Changed defaults to not display axis lines

BoutrosLab.plotting.general 3.1.14

Changed

• create.dotmap: Added 'xaxis.lab.cex' and 'yaxis.lab.cex' parameters to specify size of axis labels
• create.dotmap: Added 'key.top' parameter to specify size of space between colourkey and xaxis.label

BoutrosLab.plotting.general 3.1.13

Changed

• create.heatmap: Added 'axes.lwd' parameter to change border width

BoutrosLab.plotting.general 3.1.12

Changed

• create.multiplot: Added example combining a stripplot and heatmap

BoutrosLab.plotting.general 3.1.11

Changed

• create.heatmap: Added 'xat' and 'yat' parameters to specify label locations

BoutrosLab.plotting.general 3.1.10

Changed

• create.scatterplot: Added horizontal abline parameter - able to specify line width and type

BoutrosLab.plotting.general 3.1.9

Changed

• create.dendrogram: Added 'jaccard' option for calculating distance (for clustering discrete variables)
• create.heatmap: Added 'jaccard' option for calculating distance (for clustering discrete variables)
• create.heatmap: Added example using covariate legend

BoutrosLab.plotting.general 3.1.8

Changed

• create.heatmap: ## Changedd parameter for cell text font size & clarified definitions of 'row.lines' and 'col.lines'

BoutrosLab.plotting.general 3.1.7

Changed

• create.heatmap: Added parameters to control text in cells and to manually specify row/column grid vectors
• Legend.grob: Added parameter to specify border colour of legends

BoutrosLab.plotting.general 3.1.6

Changed

• create.multiplot: Improved legend functionality
• create.heatmap: Added ability to insert text in cells & added example

BoutrosLab.plotting.general 3.1.5

Changed

• create.heatmap: Added parameters 'title.just' and 'title.fontface' to customize legend titles

Changed

• create.heatmap: Edited documentation to finalize examples

BoutrosLab.plotting.general 3.1.4

Changed

• create.multiplot: Added parameters for more customization - 'main.cex', 'xlab.cex', 'ylab.cex', 'xlimits', 'ylimits'

BoutrosLab.plotting.general 3.1.3

Changed

• create.dendrogram: Added 'jaccard' option for calculating distance (for clustering discrete variables)
• create.heatmap: Added 'jaccard' option for calculating distance (for clustering discrete variables)
• create.heatmap: Added example using covariate legend

BoutrosLab.plotting.general 3.1.2

Changed

• create.heatmap: ## Changedd examples to be fewer and follow a logical progression
• Covariates.grob: ## Changedd examples to be generated using grid.draw() and produce .tiff output
• Legend.grob: Prevented premature closure of user images by removing "dev.off()" call & ## Changedd examples to .tiff files using grid.draw()

BoutrosLab.plotting.general 3.1.1

Changed

• create.hexbinplot: Altered layout.widths to automatically adjust key.right if colourkey is added (previously right.padding was adjusted and legend was occasionally cut off)

BoutrosLab.plotting.general 3.1.0

Added

• create.heatmap: Added ability to take more than three colours

BoutrosLab.plotting.general 3.0.9

Changed

• create.heatmap: Added parameters 'shrink', 'border', 'border.lwd'
• create.multiplot: ## Changedd example to use create.heatmap instead of base lattice::levelplot

BoutrosLab.plotting.general 3.0.8

Changed

• create.heatmap: Added parameter 'force.clustering' to allow user to ignore the row-limitation
• create.dendrogram: Added parameter 'force.clustering' to allow user to ignore the row-limitation
• Updated dependency versions

BoutrosLab.plotting.general 3.0.7

Changed

• create.histogram: ## Removed check of 'x' to ensure it is a formula - problematic is function is called within another function

BoutrosLab.plotting.general 3.0.6

Changed

• create.multiplot: Changing default of 'xaxis.alternating' parameter
• Modified "see also" documentation of plotting functions to include web versions of lattice graphics

BoutrosLab.plotting.general 3.0.5

Changed

• Added "see also" sections of documentation of plotting functions for easy referencing

BoutrosLab.plotting.general 3.0.4

Changed

• create.multiplot: Added 'panel.widths' parameter & an example to the documentation
• create.multiplot: ## Removed internal axes labels in cases where plot axes are identical
• create.scatterplot: Fixed file formatting to use tabs

BoutrosLab.plotting.general 3.0.3

Changed

• create.multiplot: Fixed file formatting to use tabs instead of spaces

BoutrosLab.plotting.general 3.0.2

Changed

• create.multiplot: Changed name of example output
• create.heatmap: Changed default colour scheme to use two colours if data is one-sided and three colours if data is two-sided

BoutrosLab.plotting.general 3.0.1

Changed

• create.heatmap: ## Changedd documentation to link to related man pages
• Legend.grob: ## Changedd documentation to explain implementation decisions

BoutrosLab.plotting.general 3.0.0

Added

• create.heatmap: Added parameters 'covariate.legends', 'legend.cex', 'legend.title.cex', and 'legend.side' to allow users to include a legend for the covariates
• Legend.grob: Added this function to draw legends

Changed

• Updated NAMESPACE to rename create.plot.with.levelplot to create.multiplot

BoutrosLab.plotting.general 2.13.1

Changed

• create.histogram: Added 'x' parameter to take in formulas, leaving 'data' parameter to take in data

BoutrosLab.plotting.general 2.13.0

Added

• create.multiplot: Renamed this function - previously called 'create.plot.with.levelplot'
• create.multiplot: ## Changedd to take any number of plots and display them in the specified layout
• create.multiplot: Replaced parameters 'plot.object' and 'levelplot.object' with 'plot.objects
• create.multiplot: Replaced parameter 'spacing' with 'yspacing'
• create.multiplot: Added parameters 'xspacing' and 'plot.layout'

BoutrosLab.plotting.general 2.12.5

Changed

• create.barplot: Added parameter 'border.col' to control border colour

BoutrosLab.plotting.general 2.12.4

Changed

• create.barplot: Added parameters 'abline.h', 'abline.type', 'abline.lwd', 'abline.col' to add superimposed line

BoutrosLab.plotting.general 2.12.3

Changed

• create.boxplot: Added parameters 'abline.h', 'abline.type', 'abline.lwd', 'abline.col' to add superimposed line

BoutrosLab.plotting.general 2.12.2

Changed

• create.barplot: Added 'panel.abline'
• create.boxplot: Added 'panel.abline'
• create.heatmap: Added parameters 'xlab', 'ylab' and ability to place x-axis label on top axis
• create.plot.with.levelplot: Added error checking for trellis objects

BoutrosLab.plotting.general 2.12.1

Changed

• create.heatmap: Added ability to plot covariates without dendrograms
• create.heatmap: Added parameters 'row.dendrogram' and 'col.dendrogram' to allow users to pass in dendrograms
• Added two functions - create.dendrogram() and covariates.grob()

BoutrosLab.plotting.general 2.12.0

Changed

• Get.defaults: Set unix to fall back on default fonts

BoutrosLab.plotting.general 2.11.10

Changed

• create.plot.with.levelplot: ## Changedd border example

BoutrosLab.plotting.general 2.11.9

• Committing new version

BoutrosLab.plotting.general 2.11.8

Changed

• create.plot.with.levelplot: Improved ability to control axis labels
• create.plot.with.levelplot: Added padding parameters

BoutrosLab.plotting.general 2.11.7

Changed

• Minor change to DESCRIPTION

BoutrosLab.plotting.general 2.11.6

Changed

• create.scatterplot: ## Changedd to allow for parameters of length one specify properties of all curves with 'add.curves' option
• create.scatterplot: Added warning for cases when curves are drawn with data containing groups where grouping variables are being ## Removed

BoutrosLab.plotting.general 2.11.5

Changed

• create.plot.with.levelplot: Reformatted example code

BoutrosLab.plotting.general 2.11.4

Changed

• create.plot.with.levelplot: Improved readability of parameter list
• create.scatterplot: ## Changedd panel.curve code to avoid 'no visible binding for global variable x' error

BoutrosLab.plotting.general 2.11.3

Changed

• create.scatterplot.with.error: Minor formatting fix to example
• create.scatterplot: Added parameter 'key.top' to control spacing above the key

BoutrosLab.plotting.general 2.11.2

Changed

• create.heatmap: Renamed parameter 'data.to.cluster' with 'x'

BoutrosLab.plotting.general 2.11.1

Changed

• create.heatmap: Cleaned up code by removing spurious print statements

BoutrosLab.plotting.general 2.11.0

Added

• Updated many plotting examples have better clarity and use default.colours()

Changed

• Default.colours: Standardized error-handling
• create.dotmap: Changed default colour scheme

BoutrosLab.plotting.general 2.10.12

Changed

• create.heatmap: Renamed parameters 'names.row' and 'names.col' with 'xaxis.lab' and 'yaxis.lab'
• create.heatmap: Added new parameter 'xaxis.col' to set colours of axis labels

BoutrosLab.plotting.general 2.10.11

Changed

• create.heatmap: Cleaned up code by standardizing variable names and adjusting error-handling

BoutrosLab.plotting.general 2.10.10

Changed

• Optimal.heatmap.cex.txt: Improved formatting of header
• create.heatmap: Cleaned up code
• create.heatmap: Added example of how to specify row and column labels

BoutrosLab.plotting.general 2.10.9

Changed

• create.scatterplot: Changed formatting to produce a smaller gap between title and plot
• create.scatterplot: ## Changedd example to include legend and filename

BoutrosLab.plotting.general 2.10.8

Changed

• create.scatterplot: Cleaned up code by removing inverted line
• Updated default value of 'strip.col' to 'white' instead of 'grey'

BoutrosLab.plotting.general 2.10.7

Changed

• create.scatterplot: Added example to draw colour depth to scatterpoints

BoutrosLab.plotting.general 2.10.6

Fixed

• create.scatterplot: Fixed ## Fixed in default behaviour for 'curve.from' and 'curve.to' parameters

Changed

• create.scatterplot: ## Changedd example

BoutrosLab.plotting.general 2.10.5

Changed

• create.scatterplot: Cleaned up code

BoutrosLab.plotting.general 2.10.4

Changed

• create.scatterplot: Replace parameter 'add.lines' with 'add.curves', this allowing the user to draw any segment of any curve that can be specified with a function
• create.scatterplot: Added example to demonstrate use of 'add.curves' parameter
• create.polygon: Fixed 'alternating' parameter to force x-axis labels to be on the bottom row
• create.polygon: ## Changedd example

BoutrosLab.plotting.general 2.10.3

Changed

• create.polygon: ## Changedd 'top.padding' and 'bottom.padding' parameters
• create.scatterplot: Added ability to draw line segments on plotting region

BoutrosLab.plotting.general 2.10.2

Changed

• create.violin.plot: ## Changedd to allow boundaries and scaling

BoutrosLab.plotting.general 2.10.1

Changed

• create.plot.with.levelplot: Added this function by merging 'create.boxplot.with.levelplot' and 'create.scatterplot.with.levelplot'

BoutrosLab.plotting.general 2.10.0

Added

• create.scatterplot.with.levelplot: Added this function

BoutrosLab.plotting.general 2.9.44

Changed

• Temporary change to lattice dependency version

BoutrosLab.plotting.general 2.9.43

Changed

• create.heatmap: Added parameters to support ?dist based distance measures for clustering
• create.hexbinplot: Added warning if specified 'maxcnt' is less than the actual max count

BoutrosLab.plotting.general 2.9.42

Changed

• create.boxplot: ## Changedd to force axis labels to always be on the left or bottom

BoutrosLab.plotting.general 2.9.41

Changed

• Added 'as.table' parameter to plotting functions to allow for panel ordering

BoutrosLab.plotting.general 2.9.40

Changed

• create.qqplot.comparison: Added option of choosing difference methods to draw a reference line
• create.qqplot.fit: Added option of choosing difference methods to draw a reference line
• create.qqplot.fit: Added ability to draw confidence bands for grouped data

BoutrosLab.plotting.general 2.9.39

Changed

• create.dotmap: Standardized parameter names

BoutrosLab.plotting.general 2.9.38

Changed

• create.dotmap: Added example of using 'padding.text'

BoutrosLab.plotting.general 2.9.37

Changed

• create.qqplot.fit: Added polygon plots for confidence intervals
• create.scatterplot: Fixed 'add.axes' parameter default value in documentation

BoutrosLab.plotting.general 2.9.36

Changed

• create.scatterplot: Changed default value of 'add.axes' parameter to FALSE
• Default.colours: Change output format to be returned, rather than printed
• create.polygon: Added 'use.loess.median' and 'use.loess.border' parameters

BoutrosLab.plotting.general 2.9.35

Changed

• Change dependency version for package BoutrosLab.statistics.general

BoutrosLab.plotting.general 2.9.34

Changed

• create.barplot: Added parameters to change colour and font size of the panel title
• create.boxplot: Added parameters to change colour and font size of the panel title
• create.polygon: Added parameters to change colour and font size of the panel title
• create.scatterplot: Added parameters to change colour and font size of the panel title

BoutrosLab.plotting.general 2.9.33

Changed

• Added 'rgb.to.greyscale' function to NAMESPACE

BoutrosLab.plotting.general 2.9.32

Fixed

• create.hexbinplot: ## Removed appearance of artificial blue dot at origin

BoutrosLab.plotting.general 2.9.31

Changed

• Rgb.to.greyscale: Added function to BoutrosLab.plotting.general

BoutrosLab.plotting.general 2.9.30

Changed

• create.qqplot.fit: Changes to ensure expected functionality

BoutrosLab.plotting.general 2.9.29

Changed

• create.qqplot.fit: Deleted function 'single.qqplot.CI' and revised corresponding part in function 'create.qqplot.fit'

BoutrosLab.plotting.general 2.9.28

Changed

• Updated maintainer email
• Removed dependency on package 'distr'

BoutrosLab.plotting.general 2.9.27

Changed

• create.histogram: Changed formatting of documentation
• create.multiple.stripplots: Added 'ylab.axis.padding' parameter

BoutrosLab.plotting.general 2.9.26

Changed

• Default.colours: Added new function to provide colour schemes for plotting

BoutrosLab.plotting.general 2.9.25

Changed

• Optimal.heatmap.cex.txt: Added lookup file for setting default font sizes for heatmaps of varying size
• create.heatmap: Changed to set default font sizes from lookup file (based on size of input)

BoutrosLab.plotting.general 2.9.24

Changed

• create.polygon: Cleaned up code

BoutrosLab.plotting.general 2.9.23

Changed

• create.multiple.boxplots: Added 'ylab.axis.padding' and 'ylab.cex' parameters

BoutrosLab.plotting.general 2.9.22

Changed

• create.dotmap: Changed default grid line colour to grey when no background colour is present

BoutrosLab.plotting.general 2.9.21

Changed

• Single.qqplot.CI: ## Removed 'subset' function

BoutrosLab.plotting.general 2.9.20

Changed

• create.qqplot.comparison: Fixed examples

BoutrosLab.plotting.general 2.9.19

Changed

• create.qqplot.comparison: Fixed examples

BoutrosLab.plotting.general 2.9.18

Changed

• create.qqplot.comparison: Added functionality of drawing confidence bands
• create.qqplot.comparison: Changed label default behaviour
• create.qqplot.fit: Changed label default behaviour
• create.dotmap: Changed default grid line colour to black if background colour is present
• create.polygon: Fixed grouping functionality and example
• create.polygon: Added translucent colours

BoutrosLab.plotting.general 2.9.17

Changed

• create.polygon: Changed input parameter settings to be more intuitive
• create.polygon: Added examples (including grouping example)

BoutrosLab.plotting.general 2.9.16

Changed

• create.scatterplot: ## Removed redundancy in code by parameterizing y=x line, and changed example

BoutrosLab.plotting.general 2.9.15

Changed

• create.boxplot.with.levelplot: Added more examples

BoutrosLab.plotting.general 2.9.14

Changed

• create.qqplot.fit: Improvements to code formatting
• create.qqplot.comparison: Improvements to code formatting
• Single.qqplot.CI: Improvements to code formatting

BoutrosLab.plotting.general 2.9.13

Changed

• create.hexbinplot: Added 'xaxis.labels' and 'yaxis.labels' parameters
• create.boxplot.with.levelplot: Improved example

BoutrosLab.plotting.general 2.9.12

Changed

• create.barplot: Added panel parameters
• create.scatterplot: Added panel parameters and improved input method of 'groups' parameter
• Boxplot.with.levelplot: Cleaned up example names
• create.polygon: Cleaned up example names

BoutrosLab.plotting.general 2.9.11

Changed

• create.scatterplot: Added 'layout' and 'xaxis.tck' parameters to specify figure arrangement and length of tick marks
• create.scatterplot: Added example to show lines connecting dots to the x-axis
• Get.corr.key: Added 'key.cex' parameter to allow users to specify font size of the key

BoutrosLab.plotting.general 2.9.10

Changed

• create.qqplot.fit: Added example
• Single.qqplot.CI: Renamed from 'qq.single.CI' and ## Changedd examples and documentation

BoutrosLab.plotting.general 2.9.9

Changed

• Qq.single.CI: Renamed from 'envelop' function
• create.qqplot.comparison: Renamed from 'create.qqplot2' function
• create.qqplot.fit: Renamed from 'create.qqplot' function
• create.scatterplot: ## Changedd example output names for consistency

BoutrosLab.plotting.general 2.9.8

Changed

• create.qqplot: Code-review
• create.qqplot2: Code-review

BoutrosLab.plotting.general 2.9.7

Changed

• Envelope: Added function to create one-sample qqplot
• create.qqplot: ## Changedd code and documentation
• create.qqplot2: ## Changedd code and documentation

BoutrosLab.plotting.general 2.9.6

Changed

• create.qqplot2: Added function to create two-sample qq plots
• create.qqplot: Added function to create one-sample qq plots
• create.boxplot.with.levelplot: ## Changedd documentation
• create.polygon: ## Changedd documentation

BoutrosLab.plotting.general 2.9.5

Changed

• create.heatmap: Added 'print.color.key' parameter to enable turning "off" of colourkey printing

BoutrosLab.plotting.general 2.9.4

Changed

• create.boxplot.with.levelplot: Added new function
• create.polygon: Added new function

BoutrosLab.plotting.general 2.9.3

Changed

• create.violin.plot: ## Changedd examples
• Updated package dependencies

BoutrosLab.plotting.general 2.9.2

Changed

• create.dotmap: ## Changedd documentation
• Updated package dependencies

BoutrosLab.plotting.general 2.9.1

Changed

• create.boxplot: Added 'x.tck' parameter to control length of tick marks

BoutrosLab.plotting.general 2.9.0

Changed

• create.dotmap: Added new plotting function

BoutrosLab.plotting.general 2.8.3

Changed

• create.boxplot: Added panel parameters
• create.heatmap: Added 'x.alternating' parameter to control position of x-axis labels
• Added warning to documentation of plotting functions to alert users of ineffective methods of running functions

BoutrosLab.plotting.general 2.8.2

Changed

• create.multiple.stripplots: Added 'type' parameter to allow users to change the type of plotting characters
• create.heatmap: Added 'xlab' and 'ylab' parameters

BoutrosLab.plotting.general 2.8.1

Changed

• create.heatmap: Added functionality of removing column and/or row grid-lines
• Updated package dependency versions

BoutrosLab.plotting.general 2.8.0

Added

• create.multiple.stripplots: Added new plotting function to create multiple stripplots

Changed

• create.multiple.boxplots: Added 'header.cex' parameter to control font size of the header

BoutrosLab.plotting.general 2.7.7

Changed

• create.violin.plot: Added 'xaxis.labels' and 'yaxis.labels' parameters to control axes labelling
• create.heatmap: Added 'top.padding' and 'bottom.padding' parameters to control top and bottom margins

BoutrosLab.plotting.general 2.7.6

Changed

• Updated plotting functions for NAMESPACE

BoutrosLab.plotting.general 2.7.5

Changed

• create.histogram: Added 'lwd' and 'lty' parameters to control line width and line style
• create.histogram: Fixed code to work without axes labels
• create.scatterplot: Added 'lty' parameter to control line style and adjusted example
• create.scatterplot.with.error: Added 'lty' parameter and adjusted example

BoutrosLab.plotting.general 2.7.4

Changed

• Added NAMESPACE

BoutrosLab.plotting.general 2.7.3

Changed

• Get.corr.key: Fixed syntax error in example
• create.boxplot: Reverted functionality to use panel.BL.bwplot
• create.scatterplot: ## Changedd examples
• create.histogram: ## Changedd examples
• create.scatterplot.with.error: ## Changedd examples
• create.violinplot: ## Changedd examples

BoutrosLab.plotting.general 2.7.2

Changed

• create.heatmap: Added 'right.padding' and 'left.padding' parameters to control margins

BoutrosLab.plotting.general 2.7.1

Changed

• Get.corr.key: Cleaned code
• create.hexbinplot: Cleaned code and fixed links in documentation

BoutrosLab.plotting.general 2.7.0

Fixed

• create.hexbinplot: Changed implementation to address critical issues related to 'maxcnt' argument

Changed

• create.hexbinplot: ## Changedd documentation with links and example
• create.barplot: ## Changedd example
• create.densityplot: ## Changedd example

BoutrosLab.plotting.general 2.6.7

Changed

• Get.corr.key: Added 'alpha.background' parameter
• create.hexbinplot: Development version - ## Fixed related to 'maxcnt' parameter

BoutrosLab.plotting.general 2.6.6

Changed

• Get.corr.key: Fixed error
• create.hexbinplot: Added 'grid' and 'abline' parameters and corresponding example

BoutrosLab.plotting.general 2.6.5

Changed

• create.hexbinplot: Added 'colorcut', 'mincnt', 'maxcnt' parameters to allow user to specify number of bins in plot

BoutrosLab.plotting.general 2.6.4

Changed

• Get.corr.key: Improved code formatting
• Get.corr.key: Added 'beta0' and 'beta1' options to the key
• create.hexbinplot: Added 'aspect' parameter to adjust plot size

BoutrosLab.plotting.general 2.6.3

Changed

• create.hexbinplot: Added 'xaxis.cex' and 'yaxis.cex' parameters

BoutrosLab.plotting.general 2.6.2

Changed

• create.boxplot: ## Changedd code to remove unnecessary dependencies
• create.boxplot: Added 'fill' parameter to control the fill colour and corresponding example
• create.scatterplot: ## Changeds to the examples

BoutrosLab.plotting.general 2.6.1

Changed

• create.dotmap: Reintroduced 'key' parameter into function
• create.dotmap: Added 'legend' parameter to allow for multiple keys

BoutrosLab.plotting.general 2.6.0

Added

• create.scatterplot: ## Changedd functionality to allow for log-scale x- and y-axes

Changed

• create.scatterplot: Cleaned up documentation

BoutrosLab.plotting.general 2.5.7

Changed

• create.densityplot: Added 'xaxis.labels' and 'yaxis.labels' parameters

BoutrosLab.plotting.general 2.5.6

Changed

• create.violin.plot: Added example using legend

BoutrosLab.plotting.general 2.5.5

Changed

• create.scatterplot.with.error: Added example using legend
• create.scatterplot: ## Changedd example

BoutrosLab.plotting.general 2.5.4

Changed

• create.hexbinplot: Added example using legend
• create.histogram: Added example using legend

BoutrosLab.plotting.general 2.5.3

Changed

• create.boxplot: Added example using legend
• create.densityplot: Added example using legend

BoutrosLab.plotting.general 2.5.2

Changed

• create.barplot.with.error: Added example using legend

BoutrosLab.plotting.general 2.5.1

Changed

• create.barplot: Added example using legend

BoutrosLab.plotting.general 2.5.0

Changed

• create.barplot.with.error: ## Changedd example

BoutrosLab.plotting.general 2.4.0

Changed

• create.dotmap: ## Removed 'legend' parameter
• create.scatterplot: ## Changedd example filenames
• create.scatterplot: Added example using legend
• create.barplot.with.error: Cleaned up code
• create.densityplot: ## Changedd code to use a single panel function

BoutrosLab.plotting.general 2.3.3

Changed

• create.heatmap: ## Changedd examples to be sequential and added example using covariates

BoutrosLab.plotting.general 2.3.2

Changed

• create.scatterplot: Added 'abline' argument
• create.scatterplot.with.error: Added 'abline' argument

BoutrosLab.plotting.general 2.3.1

Changed

• create.scatterplot: Added ability to add multiple keys to a single plot

BoutrosLab.plotting.general 2.3.0

Changed

• create.scatterplot: Cleaned up code to use a single panel function
• create.scatterplot.with.error: Cleaned up code to use a single panel function
• create.scatterplot.with.error: ## Changedd formatting to use tabs instead of spaces
• create.scatterplot.with.error: Cleaned up documentation and examples

Fixed

• create.scatterplot.with.error: Fixed ## Fixed that prevented keys from being plotted

BoutrosLab.plotting.general 2.2.0

Changed

• create.densityplot: Changed 'xat' and 'yat' parameters into 'xgrid.at' and 'ygrid.at' parameters to specify grid lines and added example
• create.scatterplot: Changed 'xat' and 'yat' parameters into 'xgrid.at' and 'ygrid.at' parameters to specify grid lines and added example
• create.scatterplot.with.error: Changed 'xat' and 'yat' parameters into 'xgrid.at' and 'ygrid.at' parameters to specify grid lines and added example

BoutrosLab.plotting.general 2.1.0

Added

• Added 'legend' and 'key' parameters to plotting functions

Changed

• create.scatterplot: Added example using a legend

BoutrosLab.plotting.general 2.0.24

Fixed

• Get.corr.key: Fixed ## Fixed related to using phantom instead of phantom(0)

BoutrosLab.plotting.general 2.0.23

Changed

• create.barplot: ## Changedd to allow use of non-factorial variables for grouping

BoutrosLab.plotting.general 2.0.22

Fixed

• create.scatterplot.with.error: Fixed error related to grid

BoutrosLab.plotting.general 2.0.21

Fixed

• create.scatterplot: Fixed error related to 'ylimits' and 'xlimits', 'yat' and 'xat
• create.scatterplot.with.error: Fixed error related to grouped line graphs

BoutrosLab.plotting.general 2.0.20

Changed

• create.barplot: Changed to prevent spurious warnings when specifying colours with ungrouped data

BoutrosLab.plotting.general 2.0.19

Changed

• create.heatmap: ## Changedd examples

BoutrosLab.plotting.general 2.0.18

Changed

• create.heatmap: Cleaned up code to remove deprecated parameter 'colour.number.tweak'

BoutrosLab.plotting.general 2.0.17

Changed

• create.scatterplot: Cleaned up examples to all use the same dataset

BoutrosLab.plotting.general 2.0.16

Changed

• create.scatterplot.with.error: Cleaned up code to match documentation

BoutrosLab.plotting.general 2.0.15

Changed

• Generate.at.final: Added function to add tick marks to plots

BoutrosLab.plotting.general 2.0.14

Changed

• Get.corr.key: Added documentation to function for automatically generating a legend with correlation, beta, and p-values

BoutrosLab.plotting.general 2.0.13

Changed

• Get.corr.key: ## Changedd to code
• Updated required packages

BoutrosLab.plotting.general 2.0.12

Changed

• Generate.at.final: Added documentation
• Get.corr.key: Added option of including beta

Fixed

• create.densityplot: Addressed problem of grid drawing and tick mark locations not lining up when both are required - this achieved by removing default grid lines and redrawing them using panel.abline() at user-specified locations

BoutrosLab.plotting.general 2.0.11

Changed

• Get.corr.key: Added flexibility to have rho in Greek
• Write.plot: Added functionality to call CairoTIFF if default tiff has problems
• create.dotmap: ## Changedd default value of 'xaxis.lab' and 'yaxis.lab' to NULL in order to accept expressions

BoutrosLab.plotting.general 2.0.10

Changed

• Get.corr.key: Added function to add basic correlation key to scatter-like plots
• create.barplot: ## Changedd documentation and examples to use more complex datasets and demonstrate use of 'ylim' and 'yat' parameters
• create.barplot: Added 'key' parameter
• create.barplot: Changed 'groups' parameter to accept an expression or variable

BoutrosLab.plotting.general 2.0.9

Changed

• create.barplot: Added filename to stacked barplot examples

Fixed

• create.barplot: Fixed problem with groups
• create.barplot.with.error: Fixed problem with groups

BoutrosLab.plotting.general 2.0.8

Changed

• create.barplot: Added user-control for colour picking for groups
• create.barplot.with.error: Added user-control for colour picking for groups
• create.barplot: Added 'group' and 'stack' parameters

BoutrosLab.plotting.general 2.0.7

Changed

• create.scatterplot: Added ability to rotate text in axis labels

BoutrosLab.plotting.general 2.0.6

Changed

• create.scatterplot.with.error: Added group-specific error bar colour handling under no conditioning

BoutrosLab.plotting.general 2.0.5

Changed

• create.scatterplot.with.error: Added 'add.axes' parameter

BoutrosLab.plotting.general 2.0.4

Changed

• create.scatterplot.with.error: Added ability to handle grouped data

BoutrosLab.plotting.general 2.0.3

Changed

• create.scatterplot: Added 'xaxis.labels' and 'yaxis.labels' parameter to allow customization of axis labels
• Get.defaults: ## Changedd to handle font changes with R v2.12.0
• create.dotmap: ## Changedd examples

BoutrosLab.plotting.general 2.0.2

Changed

• create.scatterplot: Added ability to handle grouped data

BoutrosLab.plotting.general 2.0.1

Changed

• Updated platform-specific code to work better with changes in R v2.12.0

BoutrosLab.plotting.general 2.0.0

Added

• Updated package dependencies
• Updated all plotting functions to take a main title
• Get.defaults: Fixed ## Fixed related to changes in newest versions of R and lattice
• create.heatmap: ## Changedd colouring functionality to reduce possibility of error
• create.histogram: Added functionality of colouring bars
• create.hexbinplot: Added functionality of specifying label sizes

BoutrosLab.plotting.general 1.11.2

Changed

• create.boxplot: Added 'lwd' parameter to support production of smaller images

BoutrosLab.plotting.general 1.11.1

Changed

• create.boxplot: ## Changedd to facilitate horizontal boxplots annotations for x-axis

BoutrosLab.plotting.general 1.11.0

Added

• Write.plot: Added new function to standardize plotting output - now used in all plotting functions

Changed

• create.barplot.with.error: Changed default line width of bar outline to match line width of error bar
• create.barplot: ## Changedd layout of figure to match other plotting functions
• Removed 'compression' parameter from plotting functions

BoutrosLab.plotting.general 1.10.1

Changed

• create.multiple.boxplots: Reordered parameters to be consisting with other plotting functions
• create.multiple.boxplots: Added 'symbol.cex' parameter to control size of boxplot dots

BoutrosLab.plotting.general 1.10.0

Fixed

• create.boxplot: Fixed so that 'ylimits' argument is no longer silently ignored

BoutrosLab.plotting.general 1.9.21

Changed

• create.violin.plot: ## Changedd documentation to clarify circumstances when 'x' will be coerced to a factor or shingle (when horizontal argument set to FALSE)
• create.hexbinplot: Added 'compression' and 'add.axes' parameters

BoutrosLab.plotting.general 1.9.20

Changed

• create.multiple.boxplots: ## Changedd 'right.padding' to be set to 2
• create.barplot.with.error: Renamed function from create.barplot.with.error.r into create.barplot.with.error.R

BoutrosLab.plotting.general 1.9.19

Changed

• Updated documentation of plotting functions
• Updated plotting functions to output a trellis object by default

BoutrosLab.plotting.general 1.9.18

Fixed

• create.barplot: Fixed ## Fixed that prevented implicit grouping from working
• create.barplot.with.error: Fixed ## Fixed that prevented implicit grouping from working
• create.scatterplot.with.error: Fixed ## Fixed that prevented implicit grouping from working

BoutrosLab.plotting.general 1.9.17

Fixed

• create.scatterplot: Fixed ## Fixed that prevented implicit grouping from working

BoutrosLab.plotting.general 1.9.16

Changed

• create.barplot.with.error: Added function to create barplots with customizable error bars

BoutrosLab.plotting.general 1.9.15

Changed

• create.violinplot: Added 'horizontal' parameter to allow user to specify whether to plot horizontally or vertically
• create.scatterplot.with.error: Added 'y.error.up', 'y.error.down', 'x.error.right', 'x.error.left' parameter to allow for drawing horizontal and/or vertical error bars (## Removed 'error.plus' and 'error.minus' parameters)
• create.scatterplot.with.error: Added 'x.error.bar.col' and 'y.error.bar.col' parameters
• create.scatterplot.with.error: Added 'error.whisker.angle' parameter to control the angle of whiskers drawn at both ends of the error bars

BoutrosLab.plotting.general 1.9.14

Changed

• create.boxplot: Added 'xaxis.labels' parameter

BoutrosLab.plotting.general 1.9.13

Changed

• Added warnings framework to plotting functions
• Updated functions to correctly deal with postscript graphics device
• Reimplemented fonts mechanism to support Win/*Nix systems correctly w.r.t postscript specific exceptions
• create.heatmap: Added 'cor.method' parameter

Fixed

• Panel.BL.bwplot: Fixed function to show outlier points properly when input argument box.colour is a vector

BoutrosLab.plotting.general 1.9.12

Changed

• create.barplot: ## Changedd default to give x-axis and y-axis scale labels

BoutrosLab.plotting.general 1.9.11

Changed

• Updated plotting functions to offer OS specific settings framework

BoutrosLab.plotting.general 1.9.10

Changed

• Updated plotting function documentation with "See Also" links and standardizations to the "Value" section
• create.heatmap: Renamed 'legend.cex' parameter to 'colorkey.cex'

BoutrosLab.plotting.general 1.9.9

Changed

• Updated plotting functions to have the same default font type

BoutrosLab.plotting.general 1.9.8

Fixed

• create.heatmap: Fixed functionality of 'colour.alpha' parameter

Changed

• create.heatmap: Added example to demonstrate usage of 'colour.alpha' parameter

BoutrosLab.plotting.general 1.9.7

Changed

• create.scatterplot.with.error: Added function to create scatterplot with error bars overlaid

BoutrosLab.plotting.general 1.9.6

Changed

• create.barplot: Added 'yaxis.labels' parameter
• create.scatterplot: Changed panel function to allow for ## Changed() to change conditioned trellis object
• create.multiple.boxplots: Changed c() to stack() to accommodate data.frames
• create.violin.plot: ## Changedd to match other plotting functions

BoutrosLab.plotting.general 1.9.5

Changed

• create.barplot: Added 'col' parameter to control the fill colour of bars
• create.scatterplot: Added default values for some parameters
• create.stripplot: Added default values for some parameters
• create.violinplot: Added default values for some parameters

BoutrosLab.plotting.general 1.9.4

Changed

• create.barplot: Renamed parameters to standardize with other plotting functions
• create.multiple.boxplots: Renamed parameters to standardize with other plotting functions
• create.heatmap: Added verbose warning when function cannot generate a figure
• create.boxplot: Fixed broken default handling of y-axis scale labels

BoutrosLab.plotting.general 1.9.3

Fixed

• create.heatmap: Fixed ## Fixed to accept NAs when specifying colour-ranges

BoutrosLab.plotting.general 1.9.2

Changed

• create.barplot: Changed 'xlab' and 'ylab' parameters into 'xlab.label' and 'ylab.label' and reordered parameters
• create.boxplot: Changed 'xlabel', 'ylabel', 'xlabel.cex', and 'ylabel.cex' parameters into 'xlab.lab', 'ylab.lab', 'xlab.cex', 'ylab.cex' and reordered parameters
• create.hexbinplot: Changed 'xlabel', 'ylabel' parameters into 'xlab.label', 'ylab.label'
• create.stripplot: Changed 'xlabel', 'ylabel', 'xlabel.cex', 'ylabel.cex' into 'xlab.lab', 'ylab.lab', 'xlab.cex', 'ylab.cex' and reordered parameters
• create.violinplot: Changed 'ylabel' parameter into 'ylab.label'
• create.histogram: Adjusted example
• create.multiple.boxplots: Adjusted example

BoutrosLab.plotting.general 1.9.1

Changed

• create.scatterplot: Renamed 'xlabel', 'ylabel', 'xlabel.cex', 'ylabel.cex' parameters to 'xlab.label', 'ylab.label', 'xlab.cex', 'ylab.cex'
• create.histogram: Changed default to plot percentages instead of densities
• create.scatterplot: Adjusted example to show extra ## Changed

BoutrosLab.plotting.general 1.9.0

Added

• create.densityplot: Added new function to plot densities

Changed

• create.histogram: Added many new parameters, changed order of parameters, renamed parameters for standardization
• create.boxplot: Improved example
• create.histogram: Improved example

BoutrosLab.plotting.general 1.8.1

Changed

• Updated parameter ordering of plotting functions to bring 'filename' parameter to the front of each function, and the height, width, and resolution parameters to the back

BoutrosLab.plotting.general 1.8.0

Added

• Updated plotting functions to return the trellis object only if filename = NULL
• All example files are named after the method that produced them
• Standardized variable names of plotting objects to trellis.object

Changed

• create.multiple.boxplots: Fixed spacing/indentation to match coding standard
• create.histogram: Reordered parameters to have mandatory parameters come first
• create.stripplot: Reordered parameters to have mandatory parameters come first
• create.violinplot: Reordered parameters to have mandatory parameters come first
• create.histogram: Allowed lattice default values for breaks, ylimits, etc
• create.violinplot: Allowed lattice default values for ylimits, yat

BoutrosLab.plotting.general 1.7.3

Changed

• create.heatmap: Added examples to documentation

BoutrosLab.plotting.general 1.7.2

Fixed

• create.heatmap: Fixed but in example by changing dataset
• Scientific.notation.2: Fixed function to display the last digit as 0 when requested

Changed

• create.heatmap: Added 'colorkey.labels' parameter

BoutrosLab.plotting.general 1.7.1

Changed

• create.boxplot: Renamed parameter 'ylimit' to 'ylimits' to standardize with other plotting functions
• Updates to documentation and code formatting for standardization

BoutrosLab.plotting.general 1.7.0

Added

• Propagated graphics device changes to all plotting functions - enforced graphics type to 'cairo'

BoutrosLab.plotting.general 1.6.27

Changed

• create.heatmap: Added 'at' and 'colorkey.labels.at' parameters

BoutrosLab.plotting.general 1.6.26

Changed

• create.heatmap: Enforced graphics type to 'cairo' for all platforms

BoutrosLab.plotting.general 1.6.25

Changed

• Panel.BL.bwplot: ## Changedd documentation
• create.scatterplot: Renamed 'lwdoutline' parameter to 'axis.lwd' for consistency in parameter names
• create.scatterplot: Added parameters for fontfaces of x- and y-axis scales

BoutrosLab.plotting.general 1.6.24

Changed

• create.scatterplot: ## Changedd to allow alteration of more plotting parameters and to match other plotting functions

BoutrosLab.plotting.general 1.6.23

Changed

• create.stripplot: ## Changedd to allow for alteration of more plotting parameters

BoutrosLab.plotting.general 1.6.22

Changed

• create.boxplot: ## Changedd to allow for alteration of more plotting parameters

BoutrosLab.plotting.general 1.6.21

Changed

• create.heatmap: Changed default colour.scheme from legacy parameter-handling
• create.heatmap: ## Removed spurious warnings in legacy code and added error-handling for bad usage

BoutrosLab.plotting.general 1.6.20

Changed

• create.scatterplot: Added 'compression' parameter for tiff file customization

BoutrosLab.plotting.general 1.6.19

Changed

• create.heatmap: Allowed clustering of only one dimension at a time

BoutrosLab.plotting.general 1.6.18

Changed

• create.scatterplot: Added 'lwd' parameter for best-fit lines

BoutrosLab.plotting.general 1.6.17

Changed

• create.heatmap: Changed ordering of top covariates to match right covariates
• create.heatmap: Changed axis tick-marks to be dynamic based on number of rows/columns in the heatmap

BoutrosLab.plotting.general 1.6.16

Changed

• create.scatterplot: Allowed for removal of axis-lines

BoutrosLab.plotting.general 1.6.15

Fixed

• create.boxplot: Fixed colouring issues that arose when 'box.colour' argument was passed as a vector

Changed

• Panel.BL.bwplot: Added this function to fix colouring issues with lattice::panel.bwplot()

BoutrosLab.plotting.general 1.6.14

Changed

• create.heatmap: Added 'fill.colour' parameter for background
• create.heatmap: Allowed specification of arbitrary colour-combinations

BoutrosLab.plotting.general 1.6.13

Changed

• create.heatmap: Added parameter for covariate-size

BoutrosLab.plotting.general 1.6.12

Changed

• create.heatmap: Allowed for plotting of arbitrarily large heatmaps when clustering is turned off

BoutrosLab.plotting.general 1.6.11

Changed

• create.boxplot: ## Removed pass-through parameterization because it can cause crashes when a fixed parameter is duplicated
• create.boxplot: Allowed separate sizing of axis labels and axis scales

BoutrosLab.plotting.general 1.6.10

Changed

• create.boxplot: Renamed 'box.color' to 'box.colour' to match other variables
• create.boxplot: Added 'symbol.cex' parameter to adjust outlier point size

BoutrosLab.plotting.general 1.6.9

Changed

• create.barplot: Parameterized label-sizes

BoutrosLab.plotting.general 1.6.8

Changed

• create.boxplot: Added 'box.color' parameter
• create.boxplot: ## Changedd to return a handle to plot object and added default values to input arguments
• create.multiple.boxplots: ## Changedd to get better memory efficiency

BoutrosLab.plotting.general 1.6.7

Changed

• create.barplot: Adjusted cex parameters
• create.histogram: ## Changedd to allow specification of type (percent, count, or density)
• Cleaned up documentation to reduce warnings and be more explicit

BoutrosLab.plotting.general 1.6.6

Changed

• Scientific.notation.2: ## Changedd to allow proper handling of zeros

BoutrosLab.plotting.general 1.6.5

Changed

• create.heatmap: ## Changedd to allow for adjustment of colour-range

BoutrosLab.plotting.general 1.6.4

Changed

• create.heatmap: Added selective plotting of right/top/left dendrograms
• create.heatmap: Improved colour-palette selection by calculating the range of the data
• create.heatmap: Allowed specification of main figure title
• create.heatmap: Allowed separate output of a file and/or return of a trellis object
• Enforced minimum version numbers on package dependencies

BoutrosLab.plotting.general 1.6.3

Changed

• create.heatmap: Added BlueWhiteYellow colour-scheme
• create.heatmap: ## Changedd to not run wit an invalid colour-scheme

BoutrosLab.plotting.general 1.6.2

Changed

• create.boxplot: Added option to plot or not plot outliers

BoutrosLab.plotting.general 1.6.1

Changed

• create.hexbinplot: Added new function to create hexbin plots
• create.boxplot: ## Changedd to control x- and y-axis tick sizes

BoutrosLab.plotting.general 1.5.3

Changed

• create.heatmap: Added ability to change legend size

BoutrosLab.plotting.general 1.5.2

Changed

• create.boxplot: ## Changedd so that x-axis label does not overlap with x-axis ticks

BoutrosLab.plotting.general 1.5.1

Changed

• create.boxplot: ## Changedd to be able to set label size

BoutrosLab.plotting.general 1.5.0

Added

• create.dotmap: Added new function to create dotmaps

Changed

• create.scatterplot: Added examples

BoutrosLab.plotting.general 1.4.12

Changed

• create.scatterplot: Added parameters for plot-type, point/line size, colour, and symbol

BoutrosLab.plotting.general 1.4.11

Changed

• create.barplot: Fixed handling of clustering methods other than 'none' or 'diana'
• create.heatmap: Allowed for column-wise covariates
• create.heatmap: Allowed for any agglomerative clustering method available via hclust

BoutrosLab.plotting.general 1.4.10

Changed

• create.boxplot: Allowed for rotation of x-axis names

BoutrosLab.plotting.general 1.4.9

Changed

• create.stripplot: Added new function to create strip plot

BoutrosLab.plotting.general 1.4.8

Changed

• create.barplot: Added new function to create barplot

BoutrosLab.plotting.general 1.4.7

Changed

• create.boxplot: ## Changedd to save figure directly and added example

BoutrosLab.plotting.general 1.4.6

Fixed

• create.heatmap: Fixed ## Fixed in parameter-handling that introduced spurious warnings

BoutrosLab.plotting.general 1.4.5

Changed

• create.multiple.boxplots: Modified to remove build/check warnings
• create.multiple.boxplots: Modified to ensure functionality when 'plot.names' input has less components than the 'data' input

BoutrosLab.plotting.general 1.4.4

Fixed

• create.multiple.boxplots: Fixed error where \usage called wrong function name and one argument was missing in \arguments

Added

• create.boxplot: Added new function to create boxplots

BoutrosLab.plotting.general 1.4.3

Added

• create.multiple.boxplots: Added new function to create multiple boxplots

BoutrosLab.plotting.general 1.4.2

Changed

• create.heatmap: Added ability to have clustered data without dendrograms

BoutrosLab.plotting.general 1.4.1

Changed

• create.heatmap: Added ability to handle different clustering algorithms and not plot dendrograms

BoutrosLab.plotting.general 1.4.0

Added

• create.histogram: Added function to create histograms

BoutrosLab.plotting.general 1.3.0

Added

• create.scatterplot: Added function to create scatterplots
• Scientific.notation.2: Added function to facilitate embedding of scientific notation inside other figures

BoutrosLab.plotting.general 1.2.0

Added

• Scientific.notation: Added function to allow for proper scientific notation in plots

BoutrosLab.plotting.general 1.1.0

Added

• create.heatmap: Added function to create heatmaps

BoutrosLab.plotting.general 1.0.0

Added

• Initialized package for plotting functions
• create.violin.plot: Added function to create violin plots