- 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.
- 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.
- 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