Changelog

Source: NEWS.md

gDRplots 0.99.4 - 2026-10-08

• update authors data

gDRplots 0.99.3 - 2026-10-01

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

gDRplots 0.99.2 - 2026-08-20

• update contact email addresses

gDRplots 0.99.1 - 2026-08-17

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

gDRplots 0.99.0 - 2026-08-04

• bump version to 0.99.0 for Bioconductor submission

gDRplots 0.0.119 - 2026-08-03

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

gDRplots 0.0.118 - 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 0.0.117 - 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 0.0.116 - 2026-06-23

• update pkgdown

gDRplots 0.0.115 - 2026-06-22

• update dependencies

gDRplots 0.0.114 - 2026-06-22

• update package vignette

gDRplots 0.0.113 - 2026-06-17

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

gDRplots 0.0.112 - 2026-06-16

• migrate package URLs from GitLab to GitHub

gDRplots 0.0.111 - 2026-06-16

• add LICENSE file (Artistic-2.0)

gDRplots 0.0.110 - 2026-06-11

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

gDRplots 0.0.109 - 2026-06-05

• update vignettes

gDRplots 0.0.108 - 2026-05-27

• apply updated gDRstyle rules

gDRplots 0.0.107 - 2026-04-28

• update author email address

gDRplots 0.0.106 - 2026-04-27

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

gDRplots 0.0.105 - 2026-04-23

• fix subscript out of bounds in heatmap_combo_with_isoref_panel_independent

gDRplots 0.0.104 - 2026-04-16

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

gDRplots 0.0.103 - 2026-04-08

• fix issue with returning error for boxplots

gDRplots 0.0.102 - 2026-03-16

• fix issue with negative values of iso levels

gDRplots 0.0.101 - 2026-02-18

• add boxplot by group for metrics

gDRplots 0.0.100 - 2026-01-19

• update pheatmap_qc (change standardized concentrations into unique strings)

gDRplots 0.0.99 - 2026-01-13

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

gDRplots 0.0.98 - 2026-01-02

• update x-axis label for plot_volcano_assoc_panel

gDRplots 0.0.97 - 2025-12-02

• update heatmap_combo_with_isoref_panel to work with not standard concentrations

gDRplots 0.0.96 - 2025-09-25

• add trim option in pheatmap_with_anno_x functions

gDRplots 0.0.95 - 2025-09-23

• adjust to ggplot2 v.4.0.

gDRplots 0.0.94 - 2025-08-28

• add omics prep function in reports

gDRplots 0.0.93 - 2025-08-27

• fix usage of ifelse

gDRplots 0.0.92 - 2025-08-21

• add prep function for omics data

gDRplots 0.0.91 - 2025-08-08

• fix order of boxplots in plot_boxplot_num_panel

gDRplots 0.0.90 - 2025-07-31

• add rounding options to generate_datatable
• add functions to create associations summary tables for PRISM
• add associations test data

gDRplots 0.0.89 - 2025-07-29

• update var names

gDRplots 0.0.88 - 2025-07-07

• add table as an output from plot_volcano_assoc_panel

gDRplots 0.0.87 - 2025-07-04

• update plot_dose_response_sa - option to plot only fitted curve

gDRplots 0.0.86 - 2025-07-03

• refactor create_PRISM_plot_list_sa and create_PRISM_plot_list_combo

gDRplots 0.0.85 - 2025-07-02

• add wrapper for DT::datatable

gDRplots 0.0.84 - 2025-06-25

• test data for PRISM
• update and ad dmissing tests

gDRplots 0.0.83 - 2025-06-24

• clean gene names in PRISM reports

gDRplots 0.0.82 - 2025-06-06

• update pheatmap_qc with standardized concentrations

gDRplots 0.0.81 - 2025-05-28

• update arg names in cgs functions

gDRplots 0.0.80 - 2025-05-27

• update chunk naming to fulfill knitr requirements

gDRplots 0.0.79 - 2025-05-05

• update prep_dt_depmap_feat

gDRplots 0.0.78 - 2025-04-29

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

gDRplots 0.0.77 - 2025-04-15

• add function to calculate linear associations

gDRplots 0.0.76 - 2025-04-07

• update prep_dt_depmap_meta

gDRplots 0.0.75 - 2025-03-27

• add link param in prep_plot_chunk
• add download feature in prep_plot_chunk and prep_double_table_chunk

gDRplots 0.0.74 - 2025-03-26

• handle edge-case in pheatmap_with_anno_combo

gDRplots 0.0.73 - 2025-03-25

• fix readability of number for PRISM boxplots

gDRplots 0.0.72 - 2025-03-24

• change xc50 to log10 for PRISM analysis

gDRplots 0.0.71 - 2025-03-12

• add coloring points in metric boxplots

gDRplots 0.0.70 - 2025-03-10

• update xc50 capping logic for combo PRISM inputs

gDRplots 0.0.69 - 2025-03-03

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

gDRplots 0.0.68 - 2025-02-25

• move is_color_dark from gDRiPlots package
• add .get_pheatmap_number_color function

gDRplots 0.0.67 - 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 0.0.66 - 2024-02-15

• update ls_selected_met for PRISM data

gDRplots 0.0.65 - 2024-02-12

• add support for chemical genomics analysis

gDRplots 0.0.64 - 2025-02-12

• downgrade reqs for Bioc pkgs

gDRplots 0.0.63 - 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 0.0.62 - 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 0.0.61 - 2025-02-05

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

gDRplots 0.0.60 - 2025-01-31

• fix y-axis range for dose-response curves

gDRplots 0.0.59 - 2025-01-27

• update .get_data_type with check for relation number

gDRplots 0.0.58 - 2025-01-24

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

gDRplots 0.0.57 - 2025-01-13

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

gDRplots 0.0.56 - 2022-01-13

• move ggrepel from Suggests to Imports

gDRplots 0.0.55 - 2025-01-03

• add get_r_file_path function

gDRplots 0.0.54 - 2024-12-20

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

gDRplots 0.0.53 - 2024-12-10

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

gDRplots 0.0.52 - 2024-12-09

• order subplots in plot_scatter_with_corr_panel according to given list

gDRplots 0.0.51 - 2024-12-04

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

gDRplots 0.0.50 - 2024-12-03

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

gDRplots 0.0.49 - 2024-12-02

• add boxplots for single-agent and combo metrics

gDRplots 0.0.48 - 2024-11-28

• add plate visualizations

gDRplots 0.0.47 - 2024-11-26

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

gDRplots 0.0.46 - 2024-11-25

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

gDRplots 0.0.45 - 2024-11-20

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

gDRplots 0.0.44 - 2024-11-18

• add possibility for switching axes in the combo heatmaps

gDRplots 0.0.43 - 2024-11-14

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

gDRplots 0.0.42 - 2024-11-04

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

gDRplots 0.0.41 - 2024-10-30

• update handling special characters in rmd

gDRplots 0.0.40 - 2024-10-23

• update settings.json with colors palette

gDRplots 0.0.39 - 2024-10-22

• add support for visualizing combo data without isobolograms

gDRplots 0.0.38 - 2024-10-04

• add helper functions for knitting Rmarkdown reports

gDRplots 0.0.37 - 2024-10-02

• update vignette

gDRplots 0.0.36 - 2024-09-25

• add plots and help functions for PRISM data

gDRplots 0.0.35 - 2024-09-23

• update clustering condition
• add pheatmap_with_anno_cd function

gDRplots 0.0.34 - 2024-09-16

• add clustering in pheatmap_with_anno_sa and pheatmap_with_anno_combo functions

gDRplots 0.0.33 - 2024-09-10

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

gDRplots 0.0.32 - 2024-09-09

• fix infinity values on the x-axis

gDRplots 0.0.31 - 2024-09-03

• add vignette

gDRplots 0.0.30 - 2024-08-28

• replace viridis with another set of colors

gDRplots 0.0.29 - 2024-08-23

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

gDRplots 0.0.28 - 2024-08-22

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

gDRplots 0.0.27 - 2024-08-20

• move functions related to interactive plots to the gDRiPlots package

gDRplots 0.0.26 - 2024-08-20

• make plotting functions more versatile

gDRplots 0.0.25 - 2024-08-13

• increase readability for reference isobolograms for combo data

gDRplots 0.0.24 - 2024-08-12

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

gDRplots 0.0.23 - 2024-08-09

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

gDRplots 0.0.22 - 2024-08-08

• update heatmap function to return plot and data

gDRplots 0.0.21 - 2024-08-05

• update plots for quality control of the distribution of normalized combo data

gDRplots 0.0.20 - 2024-08-05

• extend the range of x-axis in dose-response curve

gDRplots 0.0.19 - 2024-08-01

• prevent drugCombo plot from overwriting the source data

gDRplots 0.0.18 - 2024-07-26

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

gDRplots 0.0.17 - 2024-07-25

• add a function for saving plots

gDRplots 0.0.16 - 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 0.0.15 - 2024-07-16

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

gDRplots 0.0.14 - 2024-07-15

• refactor code to properly visualize data with NAs

gDRplots 0.0.13 - 2024-07-15

• fix issue with app crash when limits in create_color_palette are the same

gDRplots 0.0.12 - 2024-07-12

• move get_combo_col_settings and get_iso_colors from gDRutils package

gDRplots 0.0.11 - 2024-07-11

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

gDRplots 0.0.10 - 2024-07-10

• add plot to visualize fitting accuracy

gDRplots 0.0.9 - 2024-07-03

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

gDRplots 0.0.8 - 2024-07-01

• add function for plot size estimation

gDRplots 0.0.7 - 2024-06-21

• add plot to quality control of dose response

gDRplots 0.0.6 - 2024-06-19

• update plot function for processingReport package

gDRplots 0.0.5 - 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 0.0.4 - 2024-06-07

• update plot functions for processingReport package

gDRplots 0.0.3 - 2024-05-27

• add plot functions for processingReport package

gDRplots 0.0.2 - 2024-05-20

• move plot functions from gDRcomponents package

gDRplots 0.0.1 - 2024-05-15

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