Changes in version 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. Changes in version 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 Changes in version 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.) Changes in version 1.0.1 (2022-10-04) Update - Package title change for CRAN submission Changes in version 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 Changes in version 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) Changes in version 0.9.0 Removed - Removed ylimits and yaxis.interval parameters. (yat can be used instead.) - Removed filename parameter from SRCGrob to follow grid patterns. Changes in version 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. Changes in version 0.7.0 Update - Added yat parameter to allow specific Y axis tick values Removed - Removed yaxis.interval parameters (replaced with yat) Changes in version 0.6.0 Update - Changed output format to only return the tree grob itself (no longer including intermediate values) Changes in version 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 Changes in version 0.4.1 Update - Automatically adjusts node size, shape, and text size based on the length of the label text Changes in version 0.4.0 Update - Combined gene input dataframes into one Bug - Fixed issue when trunk node is not positioned first in the input tree Changes in version 0.3.0 Update - Allow node labels to be specified separately Bug - Fixed issue when creating ellipse nodes for longer labels Changes in version 0.2.1 Update - Allow tree input without CP and validate CP input values Changes in version 0.2.0 Update - Include tree preparation in SRCGrob to simplify use and improve consistency. Changes in version 0.1.1 Update - Remove input sampling (assume that data has been prepared properly) Changes in version 0.1.0 Update - Add functions for deep comparison of plot Grobs. - Update tests to use new comparisons and add test cases. Changes in version 0.0.0 INITIAL FEATURES - Tree, CNA, and SNV input sampling