Changes in version 2026-10-01 (2026-10-01) - make DepMap-based examples conditional on the example data being installed Changes in version 2026-08-20 (2026-08-20) - update contact email addresses Changes in version 2026-08-17 (2026-08-17) - remove alignment whitespace flagged by the gDRstyle linter - document internal helper functions with @keywords internal Changes in version 2026-08-04 (2026-08-04) - bump version to 0.99.0 for Bioconductor submission Changes in version 2026-08-03 (2026-08-03) - replace cdsrmodels dependency with inline lin_associations implementation using WGCNA and ashr Changes in version 2026-07-22 (2026-07-22) - add runnable examples to exported functions - fix BiocCheck notes (signal keyword in message, @noRd for internal functions) - add package-specific BiocCheck note filters Changes in version 2026-06-29 (2026-06-29) - replace ggpubr with patchwork for combo heatmap panels and fitting QC - add gtable/grob support in save_plot - fix combo curve plot crash for missing normalization data Changes in version 2026-06-23 (2026-06-23) - update pkgdown Changes in version 2026-06-22 (2026-06-22) - update dependencies - update package vignette Changes in version 2026-06-17 (2026-06-17) - add auto-orient combo dose-response axes by dose count Changes in version 2026-06-16 (2026-06-16) - migrate package URLs from GitLab to GitHub - add LICENSE file (Artistic-2.0) Changes in version 2026-06-11 (2026-06-11) - add auto-orient combo dose-response axes by dose count Changes in version 2026-06-05 (2026-06-05) - update vignettes Changes in version 2026-05-27 (2026-05-27) - apply updated gDRstyle rules Changes in version 2026-04-28 (2026-04-28) - update author email address Changes in version 2026-04-27 (2026-04-27) - migrate from qs to qs2 package - update batch file extension from .qs to .qs2 Changes in version 2026-04-23 (2026-04-23) - fix subscript out of bounds in heatmap_combo_with_isoref_panel_independent Changes in version 2026-04-16 (2026-04-16) - add max of y axis at 1 for dose-response curves for single-agent Changes in version 2026-04-08 (2026-04-08) - fix issue with returning error for boxplots Changes in version 2026-03-16 (2026-03-16) - fix issue with negative values of iso levels Changes in version 2026-02-18 (2026-02-18) - add boxplot by group for metrics Changes in version 2026-01-19 (2026-01-19) - update pheatmap_qc (change standardized concentrations into unique strings) Changes in version 2026-01-13 (2026-01-13) - improve QC plots for plate - add heatmaps for combo metrics data Changes in version 2026-01-02 (2026-01-02) - update x-axis label for plot_volcano_assoc_panel Changes in version 2025-12-02 (2025-12-02) - update heatmap_combo_with_isoref_panel to work with not standard concentrations Changes in version 2025-09-25 (2025-09-25) - add trim option in pheatmap_with_anno_x functions Changes in version 2025-09-23 (2025-09-23) - adjust to ggplot2 v.4.0. Changes in version 2025-08-28 (2025-08-28) - add omics prep function in reports Changes in version 2025-08-27 (2025-08-27) - fix usage of ifelse Changes in version 2025-08-21 (2025-08-21) - add prep function for omics data Changes in version 2025-08-08 (2025-08-08) - fix order of boxplots in plot_boxplot_num_panel Changes in version 2025-07-31 (2025-07-31) - add rounding options to generate_datatable - add functions to create associations summary tables for PRISM - add associations test data Changes in version 2025-07-29 (2025-07-29) - update var names Changes in version 2025-07-07 (2025-07-07) - add table as an output from plot_volcano_assoc_panel Changes in version 2025-07-04 (2025-07-04) - update plot_dose_response_sa - option to plot only fitted curve Changes in version 2025-07-03 (2025-07-03) - refactor create_PRISM_plot_list_sa and create_PRISM_plot_list_combo Changes in version 2025-07-02 (2025-07-02) - add wrapper for DT::datatable Changes in version 2025-06-25 (2025-06-25) - test data for PRISM - update and ad dmissing tests Changes in version 2025-06-24 (2025-06-24) - clean gene names in PRISM reports Changes in version 2025-06-06 (2025-06-06) - update pheatmap_qc with standardized concentrations Changes in version 2025-05-28 (2025-05-28) - update arg names in cgs functions Changes in version 2025-05-27 (2025-05-27) - update chunk naming to fulfill knitr requirements Changes in version 2025-05-05 (2025-05-05) - update prep_dt_depmap_feat Changes in version 2025-04-29 (2025-04-29) - add support for cgs analysis for difference between two cell lines Changes in version 2025-04-15 (2025-04-15) - add function to calculate linear associations Changes in version 2025-04-07 (2025-04-07) - update prep_dt_depmap_meta Changes in version 2025-03-27 (2025-03-27) - add link param in prep_plot_chunk - add download feature in prep_plot_chunk and prep_double_table_chunk Changes in version 2025-03-26 (2025-03-26) - handle edge-case in pheatmap_with_anno_combo Changes in version 2025-03-25 (2025-03-25) - fix readability of number for PRISM boxplots Changes in version 2025-03-24 (2025-03-24) - change xc50 to log10 for PRISM analysis Changes in version 2025-03-12 (2025-03-12) - add coloring points in metric boxplots Changes in version 2025-03-10 (2025-03-10) - update xc50 capping logic for combo PRISM inputs Changes in version 2025-03-03 (2025-03-03) - protect against unexpected data aggregation in data.table::dcast Changes in version 2025-02-25 (2025-02-25) - move is_color_dark from gDRiPlots package - add .get_pheatmap_number_color function Changes in version 2025-02-17 (2025-02-17) - add prep_pheatmap_matrix function - add dt_metrics_capped param to pheatmap_with_anno_sa function - update xc50 capping logic for PRISM inputs Changes in version 2025-02-12 (2025-02-12) - downgrade reqs for Bioc pkgs Changes in version 2025-02-10 (2025-02-10) - refactor plot_dose_response_sa to handle missing data consistently - fix labeling in pheatmap_qc - refactor panel shape for heatmap_combo_metrics_panel Changes in version 2025-02-06 (2025-02-06) - update plot_boxplot_meta to handle edge cases - add plot_boxplot_num and plot_boxplot_num_panel functions - add new logic for selecting n-top based on q-val and rho Changes in version 2025-02-05 (2025-02-05) - add values to combo heatmaps and adjust position of plots in the panel Changes in version 2025-01-31 (2025-01-31) - fix y-axis range for dose-response curves Changes in version 2025-01-27 (2025-01-27) - update .get_data_type with check for relation number Changes in version 2025-01-24 (2025-01-24) - update handling special characters in rmd (double colon escape) Changes in version 2025-01-13 (2025-01-13) - move compute_distances from gDRiPlots package - turn on clustering in the heatmaps with infinite and NA values Changes in version 2025-01-03 (2025-01-03) - add get_r_file_path function Changes in version 2024-12-20 (2024-12-20) - refactor prep_plot_chunk to support simple nested lists of visualizations - refactor plate visualizations to improve the performance Changes in version 2024-12-10 (2024-12-10) - refactor handling 0 in concentration column and -Inf and Inf for metrics Changes in version 2024-12-09 (2024-12-09) - order subplots in plot_scatter_with_corr_panel according to given list Changes in version 2024-12-04 (2024-12-04) - revert color palette for dose-response curves for combo data Changes in version 2024-12-03 (2024-12-03) - fix for edge-case in pheatmap_with_anno_sa (-Inf) Changes in version 2024-12-02 (2024-12-02) - add boxplots for single-agent and combo metrics Changes in version 2024-11-28 (2024-11-28) - add plate visualizations Changes in version 2024-11-26 (2024-11-26) - refactor heatmap_combo_metrics_panel function - split in single plot and panel - add plot_combination_index function Changes in version 2024-11-25 (2024-11-25) - update plot_volcano_assoc_panel - unify function name - rename heatmap_combo_metrics into heatmap_combo_metrics_panel Changes in version 2024-11-20 (2024-11-20) - add possibility for plotting isoline references for HSA Excess and Bliss Excess Changes in version 2024-11-18 (2024-11-18) - add possibility for switching axes in the combo heatmaps Changes in version 2024-11-14 (2024-11-14) - add symmetric limits on the heatmaps for Bliss and HSA excesses Changes in version 2024-11-04 (2024-11-04) - fix invalid title for dose-response curves for single-agent Changes in version 2024-10-30 (2024-10-30) - update handling special characters in rmd Changes in version 2024-10-23 (2024-10-23) - update settings.json with colors palette Changes in version 2024-10-22 (2024-10-22) - add support for visualizing combo data without isobolograms Changes in version 2024-10-04 (2024-10-04) - add helper functions for knitting Rmarkdown reports Changes in version 2024-10-02 (2024-10-02) - update vignette Changes in version 2024-09-25 (2024-09-25) - add plots and help functions for PRISM data Changes in version 2024-09-23 (2024-09-23) - update clustering condition - add pheatmap_with_anno_cd function Changes in version 2024-09-16 (2024-09-16) - add clustering in pheatmap_with_anno_sa and pheatmap_with_anno_combo functions Changes in version 2024-09-10 (2024-09-10) - increase the readability of QC dose-response curves for single-agent Changes in version 2024-09-09 (2024-09-09) - fix infinity values on the x-axis Changes in version 2024-09-03 (2024-09-03) - add vignette Changes in version 2024-08-28 (2024-08-28) - replace viridis with another set of colors Changes in version 2024-08-23 (2024-08-23) - fix bug in plot axis title - add horizontal line in 1 for dose response curve Changes in version 2024-08-22 (2024-08-22) - update heatmap function to return plot and data - change file schema Changes in version 2024-08-20 (2024-08-20) - move functions related to interactive plots to the gDRiPlots package - make plotting functions more versatile Changes in version 2024-08-13 (2024-08-13) - increase readability for reference isobolograms for combo data Changes in version 2024-08-12 (2024-08-12) - fix issue with coloring dose-response curve for combo data Changes in version 2024-08-09 (2024-08-09) - add function for neutralizing spaces in file names - add tests for rmarkdown helpers Changes in version 2024-08-08 (2024-08-08) - update heatmap function to return plot and data Changes in version 2024-08-05 (2024-08-05) - update plots for quality control of the distribution of normalized combo data - extend the range of x-axis in dose-response curve Changes in version 2024-08-01 (2024-08-01) - prevent drugCombo plot from overwriting the source data Changes in version 2024-07-26 (2024-07-26) - improve the ratio of square plots - unify text size across qc plots Changes in version 2024-07-25 (2024-07-25) - add a function for saving plots Changes in version 2024-07-24 (2024-07-24) - fix an issue with annotations coloring due to multiple occurrences - fix the lack of color for dose-response curves for single-agent in a small set of data - refactor naming for control_mapping heatmaps Changes in version 2024-07-16 (2024-07-16) - fix issue with wrong order of colorbar values for combo heatmap Changes in version 2024-07-15 (2024-07-15) - refactor code to properly visualize data with NAs - fix issue with app crash when limits in create_color_palette are the same Changes in version 2024-07-12 (2024-07-12) - move get_combo_col_settings and get_iso_colors from gDRutils package Changes in version 2024-07-11 (2024-07-11) - add plots to quality control for combo data - combo metrics and reference isoline Changes in version 2024-07-10 (2024-07-10) - add plot to visualize fitting accuracy Changes in version 2024-07-03 (2024-07-03) - add plots to quality control of distribution of normalized data and metric stat Changes in version 2024-07-01 (2024-07-01) - add function for plot size estimation Changes in version 2024-06-21 (2024-06-21) - add plot to quality control of dose response Changes in version 2024-06-19 (2024-06-19) - update plot function for processingReport package Changes in version 2024-06-14 (2024-06-14) - move plot function from metricClustering, responseGrid and metricDistribution packages - move get_metrics_to_transform, convert_factor_to_character and paletteBrew from gDRcomponents package - rename function in snake case Changes in version 2024-06-07 (2024-06-07) - update plot functions for processingReport package Changes in version 2024-05-27 (2024-05-27) - add plot functions for processingReport package Changes in version 2024-05-20 (2024-05-20) - move plot functions from gDRcomponents package Changes in version 2024-05-15 (2024-05-15) - update package structure - update SA plots and combo plots functions - add basic tests Changes in version 2024-02-15 (2024-02-15) - update ls_selected_met for PRISM data Changes in version 2024-02-12 (2024-02-12) - add support for chemical genomics analysis Changes in version 2022-01-13 (2022-01-13) - move ggrepel from Suggests to Imports