Changes in version 7.1.5 (2026-01-22) Changed - Updated maintainer contact info Changes in version 7.1.4 Fixed - Updated extra points functionality in violin plot to properly set coordinates based on plot.horizontal - Fixed unicode error in github action R CMD CHECK - Comment out filename in all help page examples. This ensures plots are rendered on our website. Added - create.violinplot panel and x-axis arguments - Parameterize title.y.coord in legend.grob() Changes in version 7.1.3 Changed - Update gleason sum colour scheme to include a colour for Gleason Sum of 10. - Update R CMD check GitHub action - Demonstrate file export in plotting function examples - Updated extra points functionality in violin plot to properly set coordinates based on plot.horizontal Changes in version 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 Changes in version 7.1.1 Changed - Improved documentation for type parameter in create.scatterplot Fixed - Fix typo in README - Update package manual for CRAN standards Changes in version 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 Changes in version 7.0.10 (2023-10-24) Changed - Add deprecation warning for test file in preparation for using testthat in the v8.0.0 release Changes in version 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 Changes in version 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() Changes in version 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label locations for continuous legends Fixed - Fix error with expressions in main for multipanelplots Removed - Remove outdated plotting data storage code Changes in version 7.0.6 Added - Add github PR template Changed - Move CICD workflow from Dockerhub to GitHub packages - Add text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 Changes in version 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 Changes in version 7.0.4 Changed - Fix border specification in create.polygonplot Changes in version 7.0.3 (2022-03-18) Changed - Update .Rbuildignore to match lab R standards Changes in version 7.0.2 Fixed - Add type comparisons for class name comparisons Changes in version 7.0.1 Fixed - Fix object protection issue in distance.c Changes in version 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() Changes in version 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 Changes in version 6.0.3 (2021-01-25) Changed - Only use cairo in the examples for covariates.grob and legend.grob if capabilities('cairo') is true. Changes in version 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 Changes in version 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 Changes in version 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 Changes in version 5.9.8 Changed - create.hexbinplot: added option to modify the default legend title Changes in version 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) Changes in version 5.9.6 Fixed - Fixed an issue that prevented extra points from plotting correctly in create.polygonplot Changes in version 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 Changes in version 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 Changes in version 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 Changes in version 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) Changes in version 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 Changes in version 5.9.0 Changed - Added code for saving data information and trellis object information to each relevant plot Changes in version 5.8.16 Changed - Cleaned up the multipanelplot code and ## Changedd the examples Changes in version 5.8.15 Changed - Made multipanelplot legend/label placement algorithm more optimal Changes in version 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 Changes in version 5.8.13 Changed - Adjusted polygon plot to work well with roc plot Changes in version 5.8.12 Changed - Added lollipop plot as an extension of scatterplot Changes in version 5.8.11 Changed - Added ability to disable factor sorting in relative plots - Added example to histogram of type change Changes in version 5.8.10 Changed - Added border colour for histogram bars Changes in version 5.8.9 Changed - Added inside legend auto finder code Fixed - Boxplot addstriplot colour was having issue with multiple boxplots, now works properly Changes in version 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 Changes in version 5.8.7 Changed - Updated formatting to match coding standard Changes in version 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 Changes in version 5.8.5 Changed - Force colour scheme now has heteroplasmy fraction and MT annotation Changes in version 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) Changes in version 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 Changes in version 5.8.2 Fixed - Completely reworked how spacing works in multipanel plot -- now creates rectangular grobs instead of using top/left/right/bottom padding Changes in version 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 Changes in version 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 Changes in version 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 Changes in version 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 Changes in version 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 Changes in version 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 Changes in version 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) Changes in version 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) Changes in version 5.6.24 Changed *create.multiplot: Added functionality to add top x-axis tick labels. Has not been extensively tested. Changes in version 5.6.23 Fixed *pcawg.colours: fixed ## Fixed that prevented project code colours from being returned. Changes in version 5.6.22 Changed *create.dotmap: addition of parameters for rectangle border thickness, rectangle border colour. Changes in version 5.6.21 Fixed - create.scatterplot: adding conditional for when pch is not referring to a point (this is in reference to KM plots) Changes in version 5.6.20 Changed - create.scatterplot: addition of parameter "col.border". This allows customizable border colours when pch >= 21. Changes in version 5.6.19 Changed - Pcawg.colours: add project.code to colour.schemes Changes in version 5.6.18 Changed - create.polygonplot: option to add rectangles. Changes in version 5.6.17 Changed - Pcawg.colours: consistent colour palette for use on pcawg data Changes in version 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 Changes in version 5.6.14 Changed - create.polygonplot: option to add text. Changes in version 5.6.13 Changed - create.polygonplot: added parameters alpha and median.lwd. Changes in version 5.6.12 Changed - create.densityplot & create.violinplot: allow adjustment of bandwidth with parameters bandwidth and bandwidth.adjust. Changes in version 5.6.11 Changed - create.stripplot: allow different border colour for added points when pch >= 21 Changes in version 5.6.10 Fixed - Reintegrated untagged changes to trunk and re-added scatterplot ## Changed Changes in version 5.6.9 Changed - create.scatterplot: allow different border colour for added points when pch >= 21 Changes in version 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. Changes in version 5.6.7 Fixed - create.multiplot: fixed ## Fixed where NULL values in parameter list (for xlimits=/ylimits=) were being ignored/unprocessed [BPG-2]. Changes in version 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] Changes in version 5.6.5 Changed - create.boxplot: Added example for adding text to plot. - create.hexbinplot: Added example of stratified multiplot. Changes in version 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. Changes in version 5.6.2 Changed - Get.cor.key: parameterizing number of decimal places to keep for spearman, pearson and kendall correlation values Changes in version 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 Changes in version 5.4.2 Changed - create.scatterplot: added option to specify colour of grid lines. Changes in version 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 Changes in version 5.3.4 Changed - create.scatterplot: ## Changedd ROC example to use auto-label placement Changes in version 5.3.3 Changed - Functions containing the word 'colour' now accept both American and Canadian spelling Changes in version 5.3.2 Fixed - create.heatmap: fixed ## Fixed which made labels disappear when stratifying dendrogram Changes in version 5.3.1 Changed - Minor Updates to the plotting guide Changes in version 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) Changes in version 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 Changes in version 5.2.19 Changed - Force.colour.scheme: added snv colour scheme Changes in version 5.2.18 Changed - Standardized all plotting functions to have resolution set to 1600 dpi - Force.colour.scheme: Added spaces in appropriate tissue names Changes in version 5.2.17 Changed - Removed out-of-date comments from examples Changes in version 5.2.16 Changed - Re-created PlottingGuide to use revamped show.available.palettes function Changes in version 5.2.13 Changed - create.multiplot: added example showing how to save parameter options from individual plots Changes in version 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) Changes in version 5.2.10 Fixed - Show.available.palettes: fixed 'general' program to no longer introduces NAs by coersion Changes in version 5.2.9 Changed - create.hexbinplot: added comment to explain maxcnt removing datapoints from example plot Changes in version 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 Changes in version 5.2.6 Changed - Write.plot: fixed ## Fixed - Added new colourkey legend and interface Changes in version 5.2.5 Changed - Updated plotting guide to have more examples and slight wording adjustments Changes in version 5.2.4 Changed - create.barplot: ablines now appear in the background of the plot instead of the foreground Changes in version 5.2.2 Changed - Write.plot: Added embed.plot functionality (depreciating said function) - Embed.plot: ## Removed embed.plot() Changes in version 5.2.1 Changed - Force.colour.scheme: ## Fixed for annovar colour schemes Changes in version 5.2.0 Changed - Added `Nature' style option to all plotting functions Changes in version 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 Changes in version 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 Changes in version 5.1.6 Changed - create.boxplot: added arguments to allow for addition of stripplot in background Changes in version 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 Changes in version 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 Changes in version 5.1.3 Changed - PlottingGuide: converting to use knitr, added further details and references to design portion - MultiPlotTutorial: deleted, contents migrated to PlottingGuide Changes in version 5.1.2 Changed - create.manhattanplot: ## Changedd documentation to use chromosome palette in force.colour.scheme Changes in version 5.1.1 Changed - create.barplot: changed default fill colour to black (instead of grey) Changes in version 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 Changes in version 5.0.28 Changed - Updated plotting guide to have extended design advice: added sections on resolution, file types, etc Changes in version 5.0.27 Changed - Updated examples in scatterplot, qqplot comparison, hexbinplot, heatmap, dotmap, and barplot to have better formatted axes labels Changes in version 5.0.26 Fixed - Re-added argument line.lwd in create.scatterplot Changes in version 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) Changes in version 5.0.24 Changed - Adjusted examples in qqplot.comparison, qqplot.fit and scatterplot to use character values for panel groupings Changes in version 5.0.23 Changed - Display.colours now additionally displays names of colours Fixed - Added 'eye' to the 'tissue' palette in force.colour.scheme Changes in version 5.0.22 Changed - Fixed: create.scatterplot, add.lines now works with lists of data Changes in version 5.0.20 Changed - Changed multiplot example to use matching gene data Changes in version 5.0.19 Changed - Changing chromosome palette in force.colour.scheme to use more visually distinct colours Changes in version 5.0.18 Fixed - Changed datasets keep common genes among datasets Changes in version 5.0.17 Changed - Updated multiplot tutorial with new examples using generate data Changes in version 5.0.16 Fixed - Default.colours: properly return the requested number of colours when multiple palettes requested Changes in version 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 Changes in version 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 Changes in version 5.0.11 Changed - Added example to create.dotmap clustered by dots and dendrogram added Changes in version 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 Changes in version 5.0.9 Changed - Formatting adjustments to examples Changes in version 5.0.8 Changed - Changed SNV dataset numerical coding to be simpler Changes in version 5.0.7 Fixed - Palettes in default.colours function properly return subsets Changes in version 5.0.6 Changed - Force.colour.scheme now accepts both upper and lower case input Changes in version 5.0.5 Changed - Changed default sequential, diverging, and binary schemes Changes in version 5.0.4 Changed - Added more schemes to default.colours Changes in version 5.0.3 Changed - Added plotting guide to vignettes Changes in version 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 Changes in version 5.0.1 Changed - Force.colour.scheme: Added colour schemes in addition to the 'annovar' schemes - Default.colours: Added additional 5-colour palette Changes in version 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 Changes in version 4.3.14 Changed - Updated test suite to remove soon-to-be deleted plotting functions Changes in version 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 Changes in version 4.3.12 Changed - create.violin.plot: ## Changedd example plots to use standard dataset Changes in version 4.3.11 Changed - create.stripplot: ## Changedd example plots to use standard dataset Changes in version 4.3.10 Changed - create.stripplot: Exposing xat and xlimits parameter to allow for customization of horizontal plots Changes in version 4.3.9 Changed - create.segplot: ## Changedd example plots to use standard dataset Changes in version 4.3.8 Changed - create.scatterplot: ## Changedd example plots to use standard dataset Changes in version 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 Changes in version 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 Changes in version 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 Changes in version 4.3.4 Changed - create.colourkey: Exposed parameter for colourkey cex Changes in version 4.3.3 Changed - create.qqplot.fit: ## Changedd example plots to use standard dataset Changes in version 4.3.2 Changed - create.qqplot.comparison: ## Changedd example plots to use standard dataset - MultiPlotTutorial: Reduced file size Changes in version 4.3.1 Changed - create.polygon: ## Changedd example plots to use standard dataset Changes in version 4.3.0 Changed - Run_plots: Added test script to package Changes in version 4.2.40 Changed - create.histogram: ## Changedd example plots to use standard dataset Changes in version 4.2.39 Changed - create.hexbinplot: ## Changedd example plots to use standard dataset Changes in version 4.2.38 Changed - create.dotmap: ## Changedd example plots to use standard dataset Changes in version 4.2.37 Changed - create.densityplot: ## Changedd example plots to use standard dataset Changes in version 4.2.36 Changed - create.boxplot: ## Changedd example plots to use standard dataset Changes in version 4.2.35 Changed - create.heatmap: ## Changedd example plots to use standard dataset Changes in version 4.2.34 Fixed - create.heatmap: Fixed error where heatmap threw error if symbols were added, but not 'border' symbols Changes in version 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 Changes in version 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 Changes in version 4.2.31 Changed - create.manhattanplot: ## Changedd example plots to use standard dataset Changes in version 4.2.30 Changed - create.barplot: ## Changedd example plots to use standard dataset Changes in version 4.2.29 Changed - create.dotmap: enabled default behaviour for NA values to plot 'X' characters size 7 Changes in version 4.2.28 Changed - create.dotmap: Improved handling of multiple pch with multiple fill colours Changes in version 4.2.27 Changed - create.dotmap: Deleted warning for using pch>=21 with lattice version 20-13 (outdated) Changes in version 4.2.26 Changed - create.dotmap: Stopped printing of warning regarding using pch>=21 with lattice version 20-13 Changes in version 4.2.25 Changed - Fixed spelling errors in documentation and code Changes in version 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 Changes in version 4.2.23 Changed - create.densityplot: Added data-sensing - create.scatterplot: Added data-sensing - create.hexbinplot: Added example of multi-colour scheme Changes in version 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 Changes in version 4.2.21 Changed - Embed.plot: Added new function to allow for plot-within-a-plot layouts Changes in version 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 Changes in version 4.2.19 Changed - Added new function 'colour.gradient' to generate sequential colour palettes Changes in version 4.2.18 Changed - create.heatmap: Added ability to stratify dendrogram - create.boxplot: Added ability to reorder boxplots based on median values Changes in version 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 Changes in version 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 Changes in version 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 Changes in version 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 Changes in version 4.2.13 Changed - create.barplot: Set default reordering to FALSE - create.dotmap: Added functionality to change dot colour Changes in version 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 Changes in version 4.2.11 Changed - Display.statistical.result: ## Changedd defaults in documentation Changes in version 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 Changes in version 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 Changes in version 4.2.8 Changed - Re-added package Changes in version 4.2.7 Added - Added create.manhattanplot function Changes in version 4.2.4 Changed - Added TODO file Changes in version 4.2.3 Changed - create.boxplot: Added ability to draw rectangle panels - create.boxplot: Added new example with grey shading between different boxes Changes in version 4.2.2 Changed - create.barplot: Added ability to change the width of the box Changes in version 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 Changes in version 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' Changes in version 4.1.8 Changed - Default.colours: ## Removed deprecated survival colour scheme - Changed warning about greyscale compatibility to be more general Changes in version 4.1.7 Changed - Default.colours: ## Removed deprecated old chromosome colour scheme - Replaced 'sandybrown' with 'tan1' in new chromosome palette Changes in version 4.1.6 Changed - Added create.colourkey to NAMESPACE Changes in version 4.1.5 Changed - Update and reorder NAMESPACE Changes in version 4.1.4 Changed - Removed unnecessary requires in get.corr.key Changes in version 4.1.3 Changed - Updated minimum required versions of dependencies Changes in version 4.1.2 Changed - create.barplot: ## Changedd manual to reflect addition of 'axis.fontface' argument - create.colourkey: ## Removed 'enable.warnings' argument Changes in version 4.1.1 Changed - create.barplot: Added arguments 'xaxis.fontface' and 'yaxis.fontface' Changes in version 4.1.0 Added - Added new function: 'create.colourkey' to generate and draw colourkey Changes in version 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 Changes in version 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 Changes in version 4.0.5 Changed - create.heatmap: Refactoring and cleanup of code Changes in version 4.0.4 Changed - create.polygon: Added 'median.lty' (for seq power plot) Changes in version 4.0.3 Changed - create.hexbinplot: Changed default of 'mincnt' to 1 (from 0) Changes in version 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' Changes in version 4.0.1 Changed - create.dotmap: Added example Changes in version 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 Changes in version 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 Changes in version 3.10.1 Changed - Legend.grob: Added ability to specify size (width) of legend boxes for each legend individually Changes in version 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 Changes in version 3.9.6 Changed - create.dotmap: Added padding parameter Changes in version 3.9.5 Changed - create.barplot: Adjustments to spacing and commenting - create.dotmap: Added ability to specify padding on all sides of plot Changes in version 3.9.4 Changed - create.multiplot: New argument 'axes.lwd' to specify border line thickness Changes in version 3.9.3 Changed - create.multiplot: Fixed 'xlab.to.xaxis.padding' variable to change the correct parameter Changes in version 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 Changes in version 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 Changes in version 3.9.0 Changed - create.multiplot: Added 'layout.skip' parameter to allow for blank spots in layout, and also added a complex example Changes in version 3.8.7 Changed - Rgb.to.greyscale: Changing function to return results, rather than print Changes in version 3.8.6 Changed - Append.footnote: Added function to create plot footnotes - Default.colours: Fixed method of returning one-colour palettes for backwards compatibility Changes in version 3.8.5 Changed - Default.colours: Adjustments to chromosome colour palette - Default.colours: Added ability to provide multiple sequential and binary colour schemes Changes in version 3.8.4 Changed - create.boxplot: Added ability to define 'abline.v' Changes in version 3.8.3 Changed - Display.colours: Added function to view colour palettes and what they look like in grey scale Changes in version 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 Changes in version 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' Changes in version 3.8.0 Added - Colour.to.grey: Added new function to convert R colours to R grey colours Changes in version 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 Changes in version 3.6.20 Changed - Get.corr.key: New arguments to allow for the addition of a title to the key Changes in version 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 Changes in version 3.6.18 Changed - create.barplot: Code clean-up to match coding standards Changes in version 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 Changes in version 3.6.16 Changed - Write.plot: Allowing pdf and png output Changes in version 3.6.15 Changed - create.segplot: Added 'abline.h' parameter Changes in version 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 Changes in version 3.6.13 Changed - create.polygon: Added line plotting options 'add.xyline', 'abline.h', 'abline.v' - create.barplot: Added examples Changes in version 3.6.12 Changed - create.multiplot: Added check for NAs in the legends workaround Changes in version 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 Changes in version 3.6.10 Changed - create.multiplot: Added 'xlab.padding', and 'key.bottom.padding' - Added copyright header to R files Changes in version 3.6.9 Changed - create.barplot: Updating with "raster" command - create.multiplot: Making examples prettier, moving key.bottom.padding into argument Changes in version 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 Changes in version 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 Changes in version 3.6.6 Changed - create.dotmap: Added argument 'pch.border.col' to set colour of dot border if pch is 21:25 Changes in version 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' Changes in version 3.6.4 Changed - create.heatmap: Added option of including x and y axis label covariates (between label and heatmap), and examples Changes in version 3.6.3 Changed - Force.colour.scheme: Added alternative colour scheme for annovar output Changes in version 3.6.2 Changed - Get.corr.key: Added missing else case for beta1.p - Force.colour.scheme: Added synonymous SNV to the list Changes in version 3.6.1 Changed - create.multiplot: Changed key.left value to 1 so that legends can be placed to left of multiplot area Changes in version 3.6.0 Added - create.scatterplot: Added ability to draw rectangles in background Changes in version 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 Changes in version 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 Changes in version 3.5.15 Changed - create.barplot: Added ability to create horizontal barplots - 'plot.horizontal', 'xlimits', and 'xat' parameters added & example Changes in version 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 Changes in version 3.5.13 Changed - Force.colour.scheme: Added overload functionality, changed scheme - Updating date with version Changes in version 3.5.12 Changed - Force.colour.scheme: Added new force colour scheme function Changed - create.barplot: Added ability to draw vertical lines Changes in version 3.5.11 Changed - create.multiplot: ## Changedd documentation to show to remove tick marks Changes in version 3.5.10 Changed - Get.line.breaks: Added get line breaks function Changes in version 3.5.9 Changed - create.heatmap: Added check for ## Changed Changes in version 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 Changes in version 3.5.7 Changed - create.dotmap: Added 'grid.col.lwd' and 'grid.row.lwd' to allow different weights of gridlines Changes in version 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 Changes in version 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 Changes in version 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 Changes in version 3.5.3 Changed - create.heatmap: Added set.seed() call at beginning of examples Changes in version 3.5.2 Changed - create.scatterplot: Fixed codoc error - General fixes for coding-style standardization and document fixes - Updates to dependency versions Changes in version 3.5.1 Changed - create.scatterplot: Changed default curves to use min/max with na.rm=T Changes in version 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 Changes in version 3.4.4 Changed - Display.statistical.result: Added space before and after "x" sign Changes in version 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 Changes in version 3.4.2 Changed - Display.statistical.result: Migrating this function to plotting.general Changes in version 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 Changes in version 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 Changes in version 3.3.7 Changed - create.segplot: ## Removed warning caused by typo in man file Changes in version 3.3.6 Changed - Legend.grob: Added code to close extra device created by the draw.key() Changes in version 3.3.5 Changed - create.densityplot: Set groups to an ordered factor (avoids auto-alphabetical ordering by lattice during plotting) Changes in version 3.3.4 Changed - create.polygon: Added example Changes in version 3.3.3 Changed - create.segplot: ## Removed unused parameter from function definition & fixed inconsistencies Changes in version 3.3.2 Changed - create.boxplot: Replaced call to panel.BL.bwplot with call to panel.bwplot Changes in version 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 Changes in version 3.3.0 Changed - create.segplot: Added new function to create segplots Changes in version 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 Changes in version 3.2.30 Changed - create.violinplot: Fixed a ## Fixed in extra points argument - create.scatterplot: Added alpha argument to control plotting transparency Changes in version 3.2.29 Changed - create.dendrogram: ## Changedd to use dist(method = "jaccard") instead of jaccard.distance() Changes in version 3.2.28 Changed - Default.colours: Changed warning message when survival colour scheme is used with more than 5 colours Changes in version 3.2.27 Changed - create.polygon: Fixed border.col argument to allow different coloured borders for multiple groups Changes in version 3.2.26 Changed - create.dendrogram: Changed jaccard.distance to use 't(x)' instead of 'x' in order to imitate behaviour of dist function Changes in version 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 Changes in version 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 Changes in version 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 Changes in version 3.2.22 Changed - Default.colours: Changed greyscale warning message for survival palette Changes in version 3.2.21 Changed - create.barplot: Added example using covariates with labels/covariate legend - create.scatterplot: Added example using covariates with labels/covariate legend Changes in version 3.2.20 Changed - create.heatmap: Resolved codoc mismatch introduced in v3.2.19 - Updated package dependencies to newer versions Changes in version 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' Changes in version 3.2.18 Changed - create.dendrogram: ## Changedd to use jaccard.distance instead of vegdist - Removed vegan dependency from DESCRIPTION Changes in version 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 Changes in version 3.2.16 Changed - Get.corr.key: Added robust regression coefficients and example using outlier - Added dependency on package MASS Changes in version 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 Changes in version 3.2.14 Changed - Default.colours: Code clean-up and added ability to use chromosome colour scheme Changes in version 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 Changes in version 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 Changes in version 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 Changes in version 3.2.10 Changed - create.heatmap: Correct ordering of text in clustered data Changes in version 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 Changes in version 3.2.8 Changed - create.stripplot: Added 'jitter' argument to allow for staggering of data along x-axis Changes in version 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 Changes in version 3.2.6 Changed - create.scatterplot: Added option 'abline.v' to draw vertical lines Changes in version 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 Changes in version 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 Changes in version 3.2.3 Changed - create.barplot: Added example with covariates Changes in version 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' Changes in version 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 Changes in version 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 Changes in version 3.1.16 Changed - create.stripplot: Implemented customizable character colour - create.multiple.stripplots: Implemented customizable character colour Changes in version 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 Changes in version 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 Changes in version 3.1.13 Changed - create.heatmap: Added 'axes.lwd' parameter to change border width Changes in version 3.1.12 Changed - create.multiplot: Added example combining a stripplot and heatmap Changes in version 3.1.11 Changed - create.heatmap: Added 'xat' and 'yat' parameters to specify label locations Changes in version 3.1.10 Changed - create.scatterplot: Added horizontal abline parameter - able to specify line width and type Changes in version 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 Changes in version 3.1.8 Changed - create.heatmap: ## Changedd parameter for cell text font size & clarified definitions of 'row.lines' and 'col.lines' Changes in version 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 Changes in version 3.1.6 Changed - create.multiplot: Improved legend functionality - create.heatmap: Added ability to insert text in cells & added example Changes in version 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 Changes in version 3.1.4 Changed - create.multiplot: Added parameters for more customization - 'main.cex', 'xlab.cex', 'ylab.cex', 'xlimits', 'ylimits' Changes in version 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 Changes in version 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() Changes in version 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) Changes in version 3.1.0 Added - create.heatmap: Added ability to take more than three colours Changes in version 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 Changes in version 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 Changes in version 3.0.7 Changed - create.histogram: ## Removed check of 'x' to ensure it is a formula - problematic is function is called within another function Changes in version 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 Changes in version 3.0.5 Changed - Added "see also" sections of documentation of plotting functions for easy referencing Changes in version 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 Changes in version 3.0.3 Changed - create.multiplot: Fixed file formatting to use tabs instead of spaces Changes in version 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 Changes in version 3.0.1 Changed - create.heatmap: ## Changedd documentation to link to related man pages - Legend.grob: ## Changedd documentation to explain implementation decisions Changes in version 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 Changes in version 2.13.1 Changed - create.histogram: Added 'x' parameter to take in formulas, leaving 'data' parameter to take in data Changes in version 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' Changes in version 2.12.5 Changed - create.barplot: Added parameter 'border.col' to control border colour Changes in version 2.12.4 Changed - create.barplot: Added parameters 'abline.h', 'abline.type', 'abline.lwd', 'abline.col' to add superimposed line Changes in version 2.12.3 Changed - create.boxplot: Added parameters 'abline.h', 'abline.type', 'abline.lwd', 'abline.col' to add superimposed line Changes in version 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 Changes in version 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() Changes in version 2.12.0 Changed - Get.defaults: Set unix to fall back on default fonts Changes in version 2.11.10 Changed - create.plot.with.levelplot: ## Changedd border example Changes in version 2.11.9 - Committing new version Changes in version 2.11.8 Changed - create.plot.with.levelplot: Improved ability to control axis labels - create.plot.with.levelplot: Added padding parameters Changes in version 2.11.7 Changed - Minor change to DESCRIPTION Changes in version 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 Changes in version 2.11.5 Changed - create.plot.with.levelplot: Reformatted example code Changes in version 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 Changes in version 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 Changes in version 2.11.2 Changed - create.heatmap: Renamed parameter 'data.to.cluster' with 'x' Changes in version 2.11.1 Changed - create.heatmap: Cleaned up code by removing spurious print statements Changes in version 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 Changes in version 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 Changes in version 2.10.11 Changed - create.heatmap: Cleaned up code by standardizing variable names and adjusting error-handling Changes in version 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 Changes in version 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 Changes in version 2.10.8 Changed - create.scatterplot: Cleaned up code by removing inverted line - Updated default value of 'strip.col' to 'white' instead of 'grey' Changes in version 2.10.7 Changed - create.scatterplot: Added example to draw colour depth to scatterpoints Changes in version 2.10.6 Fixed - create.scatterplot: Fixed ## Fixed in default behaviour for 'curve.from' and 'curve.to' parameters Changed - create.scatterplot: ## Changedd example Changes in version 2.10.5 Changed - create.scatterplot: Cleaned up code Changes in version 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 Changes in version 2.10.3 Changed - create.polygon: ## Changedd 'top.padding' and 'bottom.padding' parameters - create.scatterplot: Added ability to draw line segments on plotting region Changes in version 2.10.2 Changed - create.violin.plot: ## Changedd to allow boundaries and scaling Changes in version 2.10.1 Changed - create.plot.with.levelplot: Added this function by merging 'create.boxplot.with.levelplot' and 'create.scatterplot.with.levelplot' Changes in version 2.10.0 Added - create.scatterplot.with.levelplot: Added this function Changes in version 2.9.44 Changed - Temporary change to lattice dependency version Changes in version 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 Changes in version 2.9.42 Changed - create.boxplot: ## Changedd to force axis labels to always be on the left or bottom Changes in version 2.9.41 Changed - Added 'as.table' parameter to plotting functions to allow for panel ordering Changes in version 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 Changes in version 2.9.39 Changed - create.dotmap: Standardized parameter names Changes in version 2.9.38 Changed - create.dotmap: Added example of using 'padding.text' Changes in version 2.9.37 Changed - create.qqplot.fit: Added polygon plots for confidence intervals - create.scatterplot: Fixed 'add.axes' parameter default value in documentation Changes in version 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 Changes in version 2.9.35 Changed - Change dependency version for package BoutrosLab.statistics.general Changes in version 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 Changes in version 2.9.33 Changed - Added 'rgb.to.greyscale' function to NAMESPACE Changes in version 2.9.32 Fixed - create.hexbinplot: ## Removed appearance of artificial blue dot at origin Changes in version 2.9.31 Changed - Rgb.to.greyscale: Added function to BoutrosLab.plotting.general Changes in version 2.9.30 Changed - create.qqplot.fit: Changes to ensure expected functionality Changes in version 2.9.29 Changed - create.qqplot.fit: Deleted function 'single.qqplot.CI' and revised corresponding part in function 'create.qqplot.fit' Changes in version 2.9.28 Changed - Updated maintainer email - Removed dependency on package 'distr' Changes in version 2.9.27 Changed - create.histogram: Changed formatting of documentation - create.multiple.stripplots: Added 'ylab.axis.padding' parameter Changes in version 2.9.26 Changed - Default.colours: Added new function to provide colour schemes for plotting Changes in version 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) Changes in version 2.9.24 Changed - create.polygon: Cleaned up code Changes in version 2.9.23 Changed - create.multiple.boxplots: Added 'ylab.axis.padding' and 'ylab.cex' parameters Changes in version 2.9.22 Changed - create.dotmap: Changed default grid line colour to grey when no background colour is present Changes in version 2.9.21 Changed - Single.qqplot.CI: ## Removed 'subset' function Changes in version 2.9.20 Changed - create.qqplot.comparison: Fixed examples Changes in version 2.9.19 Changed - create.qqplot.comparison: Fixed examples Changes in version 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 Changes in version 2.9.17 Changed - create.polygon: Changed input parameter settings to be more intuitive - create.polygon: Added examples (including grouping example) Changes in version 2.9.16 Changed - create.scatterplot: ## Removed redundancy in code by parameterizing y=x line, and changed example Changes in version 2.9.15 Changed - create.boxplot.with.levelplot: Added more examples Changes in version 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 Changes in version 2.9.13 Changed - create.hexbinplot: Added 'xaxis.labels' and 'yaxis.labels' parameters - create.boxplot.with.levelplot: Improved example Changes in version 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 Changes in version 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 Changes in version 2.9.10 Changed - create.qqplot.fit: Added example - Single.qqplot.CI: Renamed from 'qq.single.CI' and ## Changedd examples and documentation Changes in version 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 Changes in version 2.9.8 Changed - create.qqplot: Code-review - create.qqplot2: Code-review Changes in version 2.9.7 Changed - Envelope: Added function to create one-sample qqplot - create.qqplot: ## Changedd code and documentation - create.qqplot2: ## Changedd code and documentation Changes in version 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 Changes in version 2.9.5 Changed - create.heatmap: Added 'print.color.key' parameter to enable turning "off" of colourkey printing Changes in version 2.9.4 Changed - create.boxplot.with.levelplot: Added new function - create.polygon: Added new function Changes in version 2.9.3 Changed - create.violin.plot: ## Changedd examples - Updated package dependencies Changes in version 2.9.2 Changed - create.dotmap: ## Changedd documentation - Updated package dependencies Changes in version 2.9.1 Changed - create.boxplot: Added 'x.tck' parameter to control length of tick marks Changes in version 2.9.0 Changed - create.dotmap: Added new plotting function Changes in version 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 Changes in version 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 Changes in version 2.8.1 Changed - create.heatmap: Added functionality of removing column and/or row grid-lines - Updated package dependency versions Changes in version 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 Changes in version 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 Changes in version 2.7.6 Changed - Updated plotting functions for NAMESPACE Changes in version 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 Changes in version 2.7.4 Changed - Added NAMESPACE Changes in version 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 Changes in version 2.7.2 Changed - create.heatmap: Added 'right.padding' and 'left.padding' parameters to control margins Changes in version 2.7.1 Changed - Get.corr.key: Cleaned code - create.hexbinplot: Cleaned code and fixed links in documentation Changes in version 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 Changes in version 2.6.7 Changed - Get.corr.key: Added 'alpha.background' parameter - create.hexbinplot: Development version - ## Fixed related to 'maxcnt' parameter Changes in version 2.6.6 Changed - Get.corr.key: Fixed error - create.hexbinplot: Added 'grid' and 'abline' parameters and corresponding example Changes in version 2.6.5 Changed - create.hexbinplot: Added 'colorcut', 'mincnt', 'maxcnt' parameters to allow user to specify number of bins in plot Changes in version 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 Changes in version 2.6.3 Changed - create.hexbinplot: Added 'xaxis.cex' and 'yaxis.cex' parameters Changes in version 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 Changes in version 2.6.1 Changed - create.dotmap: Reintroduced 'key' parameter into function - create.dotmap: Added 'legend' parameter to allow for multiple keys Changes in version 2.6.0 Added - create.scatterplot: ## Changedd functionality to allow for log-scale x- and y-axes Changed - create.scatterplot: Cleaned up documentation Changes in version 2.5.7 Changed - create.densityplot: Added 'xaxis.labels' and 'yaxis.labels' parameters Changes in version 2.5.6 Changed - create.violin.plot: Added example using legend Changes in version 2.5.5 Changed - create.scatterplot.with.error: Added example using legend - create.scatterplot: ## Changedd example Changes in version 2.5.4 Changed - create.hexbinplot: Added example using legend - create.histogram: Added example using legend Changes in version 2.5.3 Changed - create.boxplot: Added example using legend - create.densityplot: Added example using legend Changes in version 2.5.2 Changed - create.barplot.with.error: Added example using legend Changes in version 2.5.1 Changed - create.barplot: Added example using legend Changes in version 2.5.0 Changed - create.barplot.with.error: ## Changedd example Changes in version 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 Changes in version 2.3.3 Changed - create.heatmap: ## Changedd examples to be sequential and added example using covariates Changes in version 2.3.2 Changed - create.scatterplot: Added 'abline' argument - create.scatterplot.with.error: Added 'abline' argument Changes in version 2.3.1 Changed - create.scatterplot: Added ability to add multiple keys to a single plot Changes in version 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 Changes in version 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 Changes in version 2.1.0 Added - Added 'legend' and 'key' parameters to plotting functions Changed - create.scatterplot: Added example using a legend Changes in version 2.0.24 Fixed - Get.corr.key: Fixed ## Fixed related to using phantom instead of phantom(0) Changes in version 2.0.23 Changed - create.barplot: ## Changedd to allow use of non-factorial variables for grouping Changes in version 2.0.22 Fixed - create.scatterplot.with.error: Fixed error related to grid Changes in version 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 Changes in version 2.0.20 Changed - create.barplot: Changed to prevent spurious warnings when specifying colours with ungrouped data Changes in version 2.0.19 Changed - create.heatmap: ## Changedd examples Changes in version 2.0.18 Changed - create.heatmap: Cleaned up code to remove deprecated parameter 'colour.number.tweak' Changes in version 2.0.17 Changed - create.scatterplot: Cleaned up examples to all use the same dataset Changes in version 2.0.16 Changed - create.scatterplot.with.error: Cleaned up code to match documentation Changes in version 2.0.15 Changed - Generate.at.final: Added function to add tick marks to plots Changes in version 2.0.14 Changed - Get.corr.key: Added documentation to function for automatically generating a legend with correlation, beta, and p-values Changes in version 2.0.13 Changed - Get.corr.key: ## Changedd to code - Updated required packages Changes in version 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 Changes in version 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 Changes in version 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 Changes in version 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 Changes in version 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 Changes in version 2.0.7 Changed - create.scatterplot: Added ability to rotate text in axis labels Changes in version 2.0.6 Changed - create.scatterplot.with.error: Added group-specific error bar colour handling under no conditioning Changes in version 2.0.5 Changed - create.scatterplot.with.error: Added 'add.axes' parameter Changes in version 2.0.4 Changed - create.scatterplot.with.error: Added ability to handle grouped data Changes in version 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 Changes in version 2.0.2 Changed - create.scatterplot: Added ability to handle grouped data Changes in version 2.0.1 Changed - Updated platform-specific code to work better with changes in R v2.12.0 Changes in version 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 Changes in version 1.11.2 Changed - create.boxplot: Added 'lwd' parameter to support production of smaller images Changes in version 1.11.1 Changed - create.boxplot: ## Changedd to facilitate horizontal boxplots annotations for x-axis Changes in version 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 Changes in version 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 Changes in version 1.10.0 Fixed - create.boxplot: Fixed so that 'ylimits' argument is no longer silently ignored Changes in version 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 Changes in version 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 Changes in version 1.9.19 Changed - Updated documentation of plotting functions - Updated plotting functions to output a trellis object by default Changes in version 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 Changes in version 1.9.17 Fixed - create.scatterplot: Fixed ## Fixed that prevented implicit grouping from working Changes in version 1.9.16 Changed - create.barplot.with.error: Added function to create barplots with customizable error bars Changes in version 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 Changes in version 1.9.14 Changed - create.boxplot: Added 'xaxis.labels' parameter Changes in version 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 Changes in version 1.9.12 Changed - create.barplot: ## Changedd default to give x-axis and y-axis scale labels Changes in version 1.9.11 Changed - Updated plotting functions to offer OS specific settings framework Changes in version 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' Changes in version 1.9.9 Changed - Updated plotting functions to have the same default font type Changes in version 1.9.8 Fixed - create.heatmap: Fixed functionality of 'colour.alpha' parameter Changed - create.heatmap: Added example to demonstrate usage of 'colour.alpha' parameter Changes in version 1.9.7 Changed - create.scatterplot.with.error: Added function to create scatterplot with error bars overlaid Changes in version 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 Changes in version 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 Changes in version 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 Changes in version 1.9.3 Fixed - create.heatmap: Fixed ## Fixed to accept NAs when specifying colour-ranges Changes in version 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 Changes in version 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 Changes in version 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 Changes in version 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 Changes in version 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 Changes in version 1.7.3 Changed - create.heatmap: Added examples to documentation Changes in version 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 Changes in version 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 Changes in version 1.7.0 Added - Propagated graphics device changes to all plotting functions - enforced graphics type to 'cairo' Changes in version 1.6.27 Changed - create.heatmap: Added 'at' and 'colorkey.labels.at' parameters Changes in version 1.6.26 Changed - create.heatmap: Enforced graphics type to 'cairo' for all platforms Changes in version 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 Changes in version 1.6.24 Changed - create.scatterplot: ## Changedd to allow alteration of more plotting parameters and to match other plotting functions Changes in version 1.6.23 Changed - create.stripplot: ## Changedd to allow for alteration of more plotting parameters Changes in version 1.6.22 Changed - create.boxplot: ## Changedd to allow for alteration of more plotting parameters Changes in version 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 Changes in version 1.6.20 Changed - create.scatterplot: Added 'compression' parameter for tiff file customization Changes in version 1.6.19 Changed - create.heatmap: Allowed clustering of only one dimension at a time Changes in version 1.6.18 Changed - create.scatterplot: Added 'lwd' parameter for best-fit lines Changes in version 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 Changes in version 1.6.16 Changed - create.scatterplot: Allowed for removal of axis-lines Changes in version 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() Changes in version 1.6.14 Changed - create.heatmap: Added 'fill.colour' parameter for background - create.heatmap: Allowed specification of arbitrary colour-combinations Changes in version 1.6.13 Changed - create.heatmap: Added parameter for covariate-size Changes in version 1.6.12 Changed - create.heatmap: Allowed for plotting of arbitrarily large heatmaps when clustering is turned off Changes in version 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 Changes in version 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 Changes in version 1.6.9 Changed - create.barplot: Parameterized label-sizes Changes in version 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 Changes in version 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 Changes in version 1.6.6 Changed - Scientific.notation.2: ## Changedd to allow proper handling of zeros Changes in version 1.6.5 Changed - create.heatmap: ## Changedd to allow for adjustment of colour-range Changes in version 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 Changes in version 1.6.3 Changed - create.heatmap: Added BlueWhiteYellow colour-scheme - create.heatmap: ## Changedd to not run wit an invalid colour-scheme Changes in version 1.6.2 Changed - create.boxplot: Added option to plot or not plot outliers Changes in version 1.6.1 Changed - create.hexbinplot: Added new function to create hexbin plots - create.boxplot: ## Changedd to control x- and y-axis tick sizes Changes in version 1.5.3 Changed - create.heatmap: Added ability to change legend size Changes in version 1.5.2 Changed - create.boxplot: ## Changedd so that x-axis label does not overlap with x-axis ticks Changes in version 1.5.1 Changed - create.boxplot: ## Changedd to be able to set label size Changes in version 1.5.0 Added - create.dotmap: Added new function to create dotmaps Changed - create.scatterplot: Added examples Changes in version 1.4.12 Changed - create.scatterplot: Added parameters for plot-type, point/line size, colour, and symbol Changes in version 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 Changes in version 1.4.10 Changed - create.boxplot: Allowed for rotation of x-axis names Changes in version 1.4.9 Changed - create.stripplot: Added new function to create strip plot Changes in version 1.4.8 Changed - create.barplot: Added new function to create barplot Changes in version 1.4.7 Changed - create.boxplot: ## Changedd to save figure directly and added example Changes in version 1.4.6 Fixed - create.heatmap: Fixed ## Fixed in parameter-handling that introduced spurious warnings Changes in version 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 Changes in version 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 Changes in version 1.4.3 Added - create.multiple.boxplots: Added new function to create multiple boxplots Changes in version 1.4.2 Changed - create.heatmap: Added ability to have clustered data without dendrograms Changes in version 1.4.1 Changed - create.heatmap: Added ability to handle different clustering algorithms and not plot dendrograms Changes in version 1.4.0 Added - create.histogram: Added function to create histograms Changes in version 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 Changes in version 1.2.0 Added - Scientific.notation: Added function to allow for proper scientific notation in plots Changes in version 1.1.0 Added - create.heatmap: Added function to create heatmaps Changes in version 1.0.0 Added - Initialized package for plotting functions - create.violin.plot: Added function to create violin plots