NEWS

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CancerEvolutionVisualization 3.0.0

Added

• Dendrogram mode
• Optional "spread" column to control node/branch spacing
• Plotting functions to visualize the distribution of clones across the genome.
• Documentation for heatmaps and clone-genome distribution plot
• Option to disable node drawing with node-by-node control
• Node-by-node control of node size
• Aesthetic changes for heatmap and clone-genome distribution plot
• Add parameters to specify polygon shape, width, color, and transparency (alpha).
• Add option to use scale bars instead of y-axes.
• Wrapper function for SRCgrob to automatically save plots to file
• Add option to annotate the CCF summary heatmap with the cell values.
• plotting.direction argument to SRCGrob to support arbitrary direction of tree "flow". Can be one of 'down' (default), 'right', 'up', 'left' or any number (in degrees).
• Function to generate single-sample density plot
• Add support for 1xn and 1x1 heatmaps.
• Add get.colours.in.order function to get a list of colours and corresponding clone ID order.
• Add sample.order and clone.order as input parameters to create.cluster.heatmap
• Suggest rmarkdown dependency for rendering vignettes

Update

• Fixed angle calculation bug where child angles do not follow their parent angle, instead moving "downward" at 0 degrees.
• Updated package metadata and README
• Split angle handling for radial and dendrogram modes to optimized each
• Fixed bug where horizontal tree segments rendered as zero-length segments
• Updated changelog format to NEWS.md Markdown format
• Refactored use of plyr/dplyr and stringr functions to remove dependencies
• Set default parameters for heatmaps, defaulting to BPG defaults unless necessary
• Improved default node style
• Define color scheme with a single value, automatically generating other shades.
• Report the number of SNVs per clone in the legend for the clone-genome distribution plot.
• Updated the user guide to reflect new features.
• Fix bug where the x-axis only renders when y-axis is also rendered.
• Fix issue when creating polygons with more than 2 siblings
• Use updated R CMD check CI/CD action

Bug

• Resolved issue where the spread parameter was not applied in dendrogram mode.
• Resolved issue for simple dendrogram trees ( < 6 nodes or binary tree), where node angles were not calculated correctly.

CancerEvolutionVisualization 2.0.1 (2023-11-21)

Added

• GitHub links for code and bug reports

Bug

• Fixed S3 naming conflict in heatmap functions, using safe "create." prefix
• Fixed error when input is monoclonal

CancerEvolutionVisualization 2.0.0

Added

• Option to specify edge colour with "edge.col.1" and "edge.col.2" columns in tree input dataframe
• Option to specify edge width using "edge.width.1" and "edge.width.2" columns in tree input dataframe
• Option to specify edge linetype with "edge.type.1" and "edge.type.2" columns in tree input dataframe
• Support for specifying tree angles in either radians or degrees using an optional "angle" column
• Generic functions to generate accompanying heatmaps
• Option to specify tree node colours with "node.col" column
• Option to specify tree node border colour, width, and line-type with "border.col", "border.width", and "border.type" columns
• Option ot specify tree node label colour with "node.label.col" column

Update

• Reimplemented tree angle calculations
• Fixed lopsided radial tree bug

Removed

• "seg1.col" and "seg2.col" parameters (replaced by tree input columns).
• "node.col" parameter to SRCGrob. (Node colour only customizable through tree input data.frame.)

CancerEvolutionVisualization 1.0.1 (2022-10-04)

Update

• Package title change for CRAN submission

CancerEvolutionVisualization 1.0.0

Added

• Documentation for default colour scheme
• Checks for valid tree structure
  • Valid root node
  • Circular node references

Update

• Changed gene input to a generic node text input, where style and colour are specified directly (not through SNV or CNA values).
• Fixed discrepancies between documentation and code
• Fixed bug related to referencing an uninitialized variable
• Fixed y-axis positioning bug
• Updated packaging/development dependencies
• Update User Guide
• Remove README from build

CancerEvolutionVisualization 0.10.0

Added

• Optional SNV column in gene input data to italicize gene text
• Validates gene.line dist input value

Update

• Changed gene input "gene" column to more generic "name"

Removed

• Removed extra.len parameter to allow the value to be inferred by the presence/absence of CP values.
• Removed spread parameter until radial nodes are supported.
• Removed wid parameter, as it is no longer needed with horizontal.padding
• Removed cluster.list parameter until (pie nodes are implemented)

CancerEvolutionVisualization 0.9.0

Removed

• Removed ylimits and yaxis.interval parameters. (yat can be used instead.)
• Removed filename parameter from SRCGrob to follow grid patterns.

CancerEvolutionVisualization 0.8.0

Update

• Added "smart" branch length scaling based on the branch lengths and tree depth.
• The user can still scale the lengths proportionally with the scale1 and scale2 arguments.

CancerEvolutionVisualization 0.7.0

Update

• Added yat parameter to allow specific Y axis tick values

Removed

• Removed yaxis.interval parameters (replaced with yat)

CancerEvolutionVisualization 0.6.0

Update

• Changed output format to only return the tree grob itself (no longer including intermediate values)

CancerEvolutionVisualization 0.5.0

Update

• Automatically sets the branch angle to pi / 6
• Infers whether to draw polygons based on existence and changed parameter to optionally disable polygons
• Infers whether to add gene text based on presence of gene dataframe
• Changed "title" parameter names to "main"
• Separated axis parameters by X/Y axis instead of accepting a list
• Renamed "rad" parameter to "node.radius"
• Made tree input required
• Changed title unit type to a generic "unit.type" parameter to apply to any other position parameters that might be added
• Infers Y axis position based on the labels that are provided
• Changed "nodes" parameter to boolean "draw.nodes" to enable/disable node circles

Removed

• Removed the fixed_angle argument (to be replaced by an angle column in the tree input data.frame)
• Removed add.genes parameter
• Removed unused sig.curve parameter
• Disconnected pie node functionality
• Removed y.axis.position parameter
• Disabled genes.on.nodes mode

CancerEvolutionVisualization 0.4.1

Update

• Automatically adjusts node size, shape, and text size based on the length of the label text

CancerEvolutionVisualization 0.4.0

Update

• Combined gene input dataframes into one

Bug

• Fixed issue when trunk node is not positioned first in the input tree

CancerEvolutionVisualization 0.3.0

Update

• Allow node labels to be specified separately

Bug

• Fixed issue when creating ellipse nodes for longer labels

CancerEvolutionVisualization 0.2.1

Update

• Allow tree input without CP and validate CP input values

CancerEvolutionVisualization 0.2.0

Update

• Include tree preparation in SRCGrob to simplify use and improve consistency.

CancerEvolutionVisualization 0.1.1

Update

• Remove input sampling (assume that data has been prepared properly)

CancerEvolutionVisualization 0.1.0

Update

• Add functions for deep comparison of plot Grobs.
• Update tests to use new comparisons and add test cases.

CancerEvolutionVisualization 0.0.0

INITIAL FEATURES

• Tree, CNA, and SNV input sampling