- 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
SRCgrobto automatically save plots to file - Add option to annotate the CCF summary heatmap with the cell values.
plotting.directionargument toSRCGrobto 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.orderfunction to get a list of colours and corresponding clone ID order. - Add
sample.orderandclone.orderas input parameters tocreate.cluster.heatmap - Suggest rmarkdown dependency for rendering vignettes
- 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
radialanddendrogrammodes 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 checkCI/CD action
- 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.
- GitHub links for code and bug reports
- Fixed S3 naming conflict in heatmap functions, using safe "create." prefix
- Fixed error when input is monoclonal
- 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
- Reimplemented tree angle calculations
- Fixed lopsided radial tree bug
- "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.)
- Package title change for CRAN submission
- Documentation for default colour scheme
- Checks for valid tree structure
- Valid root node
- Circular node references
- 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
- Optional SNV column in gene input data to italicize gene text
- Validates gene.line dist input value
- Changed gene input "gene" column to more generic "name"
- 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)
- Removed ylimits and yaxis.interval parameters. (yat can be used instead.)
- Removed filename parameter from SRCGrob to follow grid patterns.
- 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.
- Added yat parameter to allow specific Y axis tick values
- Removed yaxis.interval parameters (replaced with yat)
- Changed output format to only return the tree grob itself (no longer including intermediate values)
- 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 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
- Automatically adjusts node size, shape, and text size based on the length of the label text
- Combined gene input dataframes into one
- Fixed issue when trunk node is not positioned first in the input tree
- Allow node labels to be specified separately
- Fixed issue when creating ellipse nodes for longer labels
- Allow tree input without CP and validate CP input values
- Include tree preparation in SRCGrob to simplify use and improve consistency.
- Remove input sampling (assume that data has been prepared properly)
- Add functions for deep comparison of plot Grobs.
- Update tests to use new comparisons and add test cases.
INITIAL FEATURES
- Tree, CNA, and SNV input sampling