NEWS

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gDRplots 2026-10-01 (2026-10-01)

• make DepMap-based examples conditional on the example data being installed

gDRplots 2026-08-20 (2026-08-20)

• update contact email addresses

gDRplots 2026-08-17 (2026-08-17)

• remove alignment whitespace flagged by the gDRstyle linter
• document internal helper functions with @keywords internal

gDRplots 2026-08-04 (2026-08-04)

• bump version to 0.99.0 for Bioconductor submission

gDRplots 2026-08-03 (2026-08-03)

• replace cdsrmodels dependency with inline lin_associations implementation using WGCNA and ashr

gDRplots 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

gDRplots 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

gDRplots 2026-06-23 (2026-06-23)

• update pkgdown

gDRplots 2026-06-22 (2026-06-22)

• update dependencies

• update package vignette

gDRplots 2026-06-17 (2026-06-17)

• add auto-orient combo dose-response axes by dose count

gDRplots 2026-06-16 (2026-06-16)

• migrate package URLs from GitLab to GitHub

• add LICENSE file (Artistic-2.0)

gDRplots 2026-06-11 (2026-06-11)

• add auto-orient combo dose-response axes by dose count

gDRplots 2026-06-05 (2026-06-05)

• update vignettes

gDRplots 2026-05-27 (2026-05-27)

• apply updated gDRstyle rules

gDRplots 2026-04-28 (2026-04-28)

• update author email address

gDRplots 2026-04-27 (2026-04-27)

• migrate from qs to qs2 package
• update batch file extension from .qs to .qs2

gDRplots 2026-04-23 (2026-04-23)

• fix subscript out of bounds in heatmap_combo_with_isoref_panel_independent

gDRplots 2026-04-16 (2026-04-16)

• add max of y axis at 1 for dose-response curves for single-agent

gDRplots 2026-04-08 (2026-04-08)

• fix issue with returning error for boxplots

gDRplots 2026-03-16 (2026-03-16)

• fix issue with negative values of iso levels

gDRplots 2026-02-18 (2026-02-18)

• add boxplot by group for metrics

gDRplots 2026-01-19 (2026-01-19)

• update pheatmap_qc (change standardized concentrations into unique strings)

gDRplots 2026-01-13 (2026-01-13)

• improve QC plots for plate
• add heatmaps for combo metrics data

gDRplots 2026-01-02 (2026-01-02)

• update x-axis label for plot_volcano_assoc_panel

gDRplots 2025-12-02 (2025-12-02)

• update heatmap_combo_with_isoref_panel to work with not standard concentrations

gDRplots 2025-09-25 (2025-09-25)

• add trim option in pheatmap_with_anno_x functions

gDRplots 2025-09-23 (2025-09-23)

• adjust to ggplot2 v.4.0.

gDRplots 2025-08-28 (2025-08-28)

• add omics prep function in reports

gDRplots 2025-08-27 (2025-08-27)

• fix usage of ifelse

gDRplots 2025-08-21 (2025-08-21)

• add prep function for omics data

gDRplots 2025-08-08 (2025-08-08)

• fix order of boxplots in plot_boxplot_num_panel

gDRplots 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

gDRplots 2025-07-29 (2025-07-29)

• update var names

gDRplots 2025-07-07 (2025-07-07)

• add table as an output from plot_volcano_assoc_panel

gDRplots 2025-07-04 (2025-07-04)

• update plot_dose_response_sa - option to plot only fitted curve

gDRplots 2025-07-03 (2025-07-03)

• refactor create_PRISM_plot_list_sa and create_PRISM_plot_list_combo

gDRplots 2025-07-02 (2025-07-02)

• add wrapper for DT::datatable

gDRplots 2025-06-25 (2025-06-25)

• test data for PRISM
• update and ad dmissing tests

gDRplots 2025-06-24 (2025-06-24)

• clean gene names in PRISM reports

gDRplots 2025-06-06 (2025-06-06)

• update pheatmap_qc with standardized concentrations

gDRplots 2025-05-28 (2025-05-28)

• update arg names in cgs functions

gDRplots 2025-05-27 (2025-05-27)

• update chunk naming to fulfill knitr requirements

gDRplots 2025-05-05 (2025-05-05)

• update prep_dt_depmap_feat

gDRplots 2025-04-29 (2025-04-29)

• add support for cgs analysis for difference between two cell lines

gDRplots 2025-04-15 (2025-04-15)

• add function to calculate linear associations

gDRplots 2025-04-07 (2025-04-07)

• update prep_dt_depmap_meta

gDRplots 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

gDRplots 2025-03-26 (2025-03-26)

• handle edge-case in pheatmap_with_anno_combo

gDRplots 2025-03-25 (2025-03-25)

• fix readability of number for PRISM boxplots

gDRplots 2025-03-24 (2025-03-24)

• change xc50 to log10 for PRISM analysis

gDRplots 2025-03-12 (2025-03-12)

• add coloring points in metric boxplots

gDRplots 2025-03-10 (2025-03-10)

• update xc50 capping logic for combo PRISM inputs

gDRplots 2025-03-03 (2025-03-03)

• protect against unexpected data aggregation in data.table::dcast

gDRplots 2025-02-25 (2025-02-25)

• move is_color_dark from gDRiPlots package
• add .get_pheatmap_number_color function

gDRplots 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

gDRplots 2025-02-12 (2025-02-12)

• downgrade reqs for Bioc pkgs

gDRplots 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

gDRplots 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

gDRplots 2025-02-05 (2025-02-05)

• add values to combo heatmaps and adjust position of plots in the panel

gDRplots 2025-01-31 (2025-01-31)

• fix y-axis range for dose-response curves

gDRplots 2025-01-27 (2025-01-27)

• update .get_data_type with check for relation number

gDRplots 2025-01-24 (2025-01-24)

• update handling special characters in rmd (double colon escape)

gDRplots 2025-01-13 (2025-01-13)

• move compute_distances from gDRiPlots package
• turn on clustering in the heatmaps with infinite and NA values

gDRplots 2025-01-03 (2025-01-03)

• add get_r_file_path function

gDRplots 2024-12-20 (2024-12-20)

• refactor prep_plot_chunk to support simple nested lists of visualizations
• refactor plate visualizations to improve the performance

gDRplots 2024-12-10 (2024-12-10)

• refactor handling 0 in concentration column and -Inf and Inf for metrics

gDRplots 2024-12-09 (2024-12-09)

• order subplots in plot_scatter_with_corr_panel according to given list

gDRplots 2024-12-04 (2024-12-04)

• revert color palette for dose-response curves for combo data

gDRplots 2024-12-03 (2024-12-03)

• fix for edge-case in pheatmap_with_anno_sa (-Inf)

gDRplots 2024-12-02 (2024-12-02)

• add boxplots for single-agent and combo metrics

gDRplots 2024-11-28 (2024-11-28)

• add plate visualizations

gDRplots 2024-11-26 (2024-11-26)

• refactor heatmap_combo_metrics_panel function - split in single plot and panel
• add plot_combination_index function

gDRplots 2024-11-25 (2024-11-25)

• update plot_volcano_assoc_panel
• unify function name - rename heatmap_combo_metrics into heatmap_combo_metrics_panel

gDRplots 2024-11-20 (2024-11-20)

• add possibility for plotting isoline references for HSA Excess and Bliss Excess

gDRplots 2024-11-18 (2024-11-18)

• add possibility for switching axes in the combo heatmaps

gDRplots 2024-11-14 (2024-11-14)

• add symmetric limits on the heatmaps for Bliss and HSA excesses

gDRplots 2024-11-04 (2024-11-04)

• fix invalid title for dose-response curves for single-agent

gDRplots 2024-10-30 (2024-10-30)

• update handling special characters in rmd

gDRplots 2024-10-23 (2024-10-23)

• update settings.json with colors palette

gDRplots 2024-10-22 (2024-10-22)

• add support for visualizing combo data without isobolograms

gDRplots 2024-10-04 (2024-10-04)

• add helper functions for knitting Rmarkdown reports

gDRplots 2024-10-02 (2024-10-02)

• update vignette

gDRplots 2024-09-25 (2024-09-25)

• add plots and help functions for PRISM data

gDRplots 2024-09-23 (2024-09-23)

• update clustering condition
• add pheatmap_with_anno_cd function

gDRplots 2024-09-16 (2024-09-16)

• add clustering in pheatmap_with_anno_sa and pheatmap_with_anno_combo functions

gDRplots 2024-09-10 (2024-09-10)

• increase the readability of QC dose-response curves for single-agent

gDRplots 2024-09-09 (2024-09-09)

• fix infinity values on the x-axis

gDRplots 2024-09-03 (2024-09-03)

• add vignette

gDRplots 2024-08-28 (2024-08-28)

• replace viridis with another set of colors

gDRplots 2024-08-23 (2024-08-23)

• fix bug in plot axis title
• add horizontal line in 1 for dose response curve

gDRplots 2024-08-22 (2024-08-22)

• update heatmap function to return plot and data - change file schema

gDRplots 2024-08-20 (2024-08-20)

• move functions related to interactive plots to the gDRiPlots package

• make plotting functions more versatile

gDRplots 2024-08-13 (2024-08-13)

• increase readability for reference isobolograms for combo data

gDRplots 2024-08-12 (2024-08-12)

• fix issue with coloring dose-response curve for combo data

gDRplots 2024-08-09 (2024-08-09)

• add function for neutralizing spaces in file names
• add tests for rmarkdown helpers

gDRplots 2024-08-08 (2024-08-08)

• update heatmap function to return plot and data

gDRplots 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

gDRplots 2024-08-01 (2024-08-01)

• prevent drugCombo plot from overwriting the source data

gDRplots 2024-07-26 (2024-07-26)

• improve the ratio of square plots
• unify text size across qc plots

gDRplots 2024-07-25 (2024-07-25)

• add a function for saving plots

gDRplots 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

gDRplots 2024-07-16 (2024-07-16)

• fix issue with wrong order of colorbar values for combo heatmap

gDRplots 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

gDRplots 2024-07-12 (2024-07-12)

• move get_combo_col_settings and get_iso_colors from gDRutils package

gDRplots 2024-07-11 (2024-07-11)

• add plots to quality control for combo data - combo metrics and reference isoline

gDRplots 2024-07-10 (2024-07-10)

• add plot to visualize fitting accuracy

gDRplots 2024-07-03 (2024-07-03)

• add plots to quality control of distribution of normalized data and metric stat

gDRplots 2024-07-01 (2024-07-01)

• add function for plot size estimation

gDRplots 2024-06-21 (2024-06-21)

• add plot to quality control of dose response

gDRplots 2024-06-19 (2024-06-19)

• update plot function for processingReport package

gDRplots 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

gDRplots 2024-06-07 (2024-06-07)

• update plot functions for processingReport package

gDRplots 2024-05-27 (2024-05-27)

• add plot functions for processingReport package

gDRplots 2024-05-20 (2024-05-20)

• move plot functions from gDRcomponents package

gDRplots 2024-05-15 (2024-05-15)

• update package structure
• update SA plots and combo plots functions
• add basic tests

gDRplots 2024-02-15 (2024-02-15)

• update ls_selected_met for PRISM data

gDRplots 2024-02-12 (2024-02-12)

• add support for chemical genomics analysis

gDRplots 2022-01-13 (2022-01-13)

• move ggrepel from Suggests to Imports