CancerEvolutionVisualization 2.0.1 2023-11-17 (Helena Winata, Dan Knight) ADDED * GitHub links for code and bug reports BUG * Fixed S3 naming conflict in heatmap functions, using safe "create." prefix -------------------------------------------------------------------------- CancerEvolutionVisualization 2.0.0 2023-11-16 (Helena Winata, Dan Knight) 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 2022-10-03 (Dan Knight) UPDATE * Package title change for CRAN submission -------------------------------------------------------------------------- CancerEvolutionVisualization 1.0.0 2022-09-28 (Dan Knight) 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 2022-08-01 (Dan Knight) 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 2022-07-20 (Dan Knight) 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 2022-07-14 (Dan Knight) 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 2022-06-28 (Dan Knight) UPDATE * Added yat parameter to allow specific Y axis tick values REMOVED * Removed yaxis.interval parameters (replaced with yat) -------------------------------------------------------------------------- CancerEvolutionVisualization 0.6.0 2022-06-24 (Dan Knight) UPDATE * Changed output format to only return the tree grob itself (no longer including intermediate values) -------------------------------------------------------------------------- CancerEvolutionVisualization 0.5.0 2022-06-24 (Dan Knight) 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 2022-05-05 (Dan Knight) UPDATE * Automatically adjusts node size, shape, and text size based on the length of the label text -------------------------------------------------------------------------- CancerEvolutionVisualization 0.4.0 2022-05-03 (Dan Knight) 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 2022-04-29 (Dan Knight) UPDATE * Allow node labels to be specified separately BUG * Fixed issue when creating ellipse nodes for longer labels -------------------------------------------------------------------------- CancerEvolutionVisualization 0.2.1 2022-04-14 (Dan Knight) UPDATE * Allow tree input without CP and validate CP input values -------------------------------------------------------------------------- CancerEvolutionVisualization 0.2.0 2022-04-12 (Dan Knight) UPDATE * Include tree preparation in SRCGrob to simplify use and improve consistency. -------------------------------------------------------------------------- CancerEvolutionVisualization 0.1.1 2022-02-23 (Dan Knight) UPDATE * Remove input sampling (assume that data has been prepared properly) -------------------------------------------------------------------------- CancerEvolutionVisualization 0.1.0 2021-11-08 (Dan Knight) UPDATE * Add functions for deep comparison of plot Grobs. * Update tests to use new comparisons and add test cases. -------------------------------------------------------------------------- CancerEvolutionVisualization 0.0.0 2021-09-13 (Adriana Salcedo) INITIAL FEATURES - Tree, CNA, and SNV input sampling