Package: gDRplots 0.99.3

Arkadiusz Gladki

gDRplots: 'gDRplots'

gDRplots provides static visualization functions and dedicated helpers for the gDR drug response platform. Designed for high-throughput screening (HTS), pharmacogenomics, and chemical genomics research, it enables comprehensive analysis of single-agent, co-dilution, and drug combination cell viability assays. The package supports quality control (plate layouts, control mapping), data normalization inspection, dose-response curves, distribution boxplots, drug synergy heatmaps with overlaid isobolograms, and combination index plots. Additionally, it integrates with PRISM and DepMap datasets to generate volcano plots and correlation scatter plots for molecular feature associations.

Authors:Marc Hafner [aut], Janina Smola [aut], Bartosz Czech [aut], Dariusz Scigocki [aut], Arkadiusz Gladki [aut, cre]

gDRplots_0.99.3.tar.gz
gDRplots_0.99.3.zip(r-4.7-any)gDRplots_0.99.3.zip(r-4.6-any)gDRplots_0.99.3.zip(r-4.5-any)
gDRplots_0.99.3.tgz(r-4.6-any)gDRplots_0.99.3.tgz(r-4.5-any)
gDRplots_0.99.3.tar.gz(r-4.7-any)gDRplots_0.99.3.tar.gz(r-4.6-any)
gDRplots_0.99.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
gDRplots/json (API)

# Install 'gDRplots' in R:

install.packages('gDRplots', repos = c('https://biocstaging.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/gdrplatform/gdrplots/issues

Pkgdown/docs site:https://gdrplatform.github.io

On CRAN:

software visualization qualitycontrol normalization cellbasedassays pharmacogenomics microtitreplateassay

4.49 score 26 scripts 80 exports 171 dependencies

Last updated from:04d0c5c7aa. Checks:1 WARNING, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	226
linux-devel	OK	748
source / vignettes	OK	411
linux-release	OK	697
macos-release	OK	2186
macos-oldrel	OK	771
windows-devel	OK	769
windows-release	OK	809
windows-oldrel	OK	770
wasm-release	OK	218

Exports:analyze_cgs calc_assoc change_NA_into_char compute_distances create_download_link create_log_seq create_PRISM_plot_list_combo create_PRISM_plot_list_sa create_PRISM_summary_list create_zoom_link escape_special_characters estimate_plot_size fill_ann_color_map generate_datatable get_ann_color_map get_col_luminance get_hm_title get_iso_colors get_qual_colors get_r_file_path heatmap_combo_metrics heatmap_combo_metrics_panel heatmap_combo_with_isoref heatmap_combo_with_isoref_panel heatmap_combo_with_isoref_panel_common heatmap_combo_with_isoref_panel_independent heatmap_control_mapping_qc is_color_dark is_valid_color neutralize_spaces pheatmap_qc pheatmap_with_anno_cd pheatmap_with_anno_combo pheatmap_with_anno_combo_metrics pheatmap_with_anno_sa plot_boxplot_meta plot_boxplot_metric_combo plot_boxplot_metric_combo_by_CLs plot_boxplot_metric_combo_by_drugs plot_boxplot_metric_combo_by_grp plot_boxplot_metric_sa plot_boxplot_metric_sa_by_CLs plot_boxplot_metric_sa_by_drugs plot_boxplot_metric_sa_by_grp plot_boxplot_num plot_boxplot_num_panel plot_cgs_ranking plot_combination_index plot_dose_response_combo plot_dose_response_combo_panel plot_dose_response_sa plot_dose_response_sa_by_CLs plot_dose_response_sa_by_drugs plot_dose_response_sa_qc plot_dose_response_sa_qc_panel plot_fitting_acc plot_plate plot_plate_stack_info plot_scatter_with_corr plot_scatter_with_corr_panel plot_single_plate_stack_info plot_var_distribution_qc plot_var_stat_qc plot_volcano_assoc plot_volcano_assoc_panel prep_assoc_summary prep_double_table_chunk prep_dt_assoc prep_dt_depmap_feat prep_dt_depmap_meta prep_dt_response_dose_sa prep_dt_response_metric_diff prep_dt_response_metric_sa prep_dt_response_scores prep_filename_path prep_nested_plot_chunk prep_pheatmap_matrix prep_plot_chunk round_to_unique_string save_plot

Dependencies:abind ashr backports base64enc BH Biobase BiocBaseUtils BiocGenerics BiocParallel boot broom bslib BumpyMatrix cachem car carData checkmate cli cluster codetools colorspace commonmark cowplot cpp11 crosstalk curl data.table DelayedArray Deriv digest doBy doParallel dplyr drc DT dynamicTreeCut etrunct evaluate farver fastcluster fastmap fastmatch fgsea fontawesome foreach forecast foreign formatR Formula fracdiff fs futile.logger futile.options gDRutils generics GenomicRanges ggplot2 ggrepel ggtext glue gridExtra gridtext gtable gtools highr Hmisc htmlTable htmltools htmlwidgets impute invgamma IRanges irlba isoband iterators jpeg jquerylib jsonlite jsonvalidate knitr labeling lambda.r later lattice lazyeval lifecycle litedown lme4 lmtest magrittr markdown MASS Matrix MatrixGenerics MatrixModels matrixStats memoise mgcv mime minqa mixsqp modelr multcomp MultiAssayExperiment mvtnorm nlme nloptr nnet numDeriv otel patchwork pbkrtest pheatmap pillar pkgconfig plotrix png preprocessCore promises purrr qs2 quantreg R6 rappdirs rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen RcppParallel Rdpack reformulas rlang rmarkdown rpart rstudioapi S4Arrays S4Vectors S7 sandwich sass scales Seqinfo snow SparseArray SparseM SQUAREM stringfish stringi stringr SummarizedExperiment survival TH.data tibble tidyr tidyselect timeDate tinytex truncnorm urca utf8 V8 vctrs viridisLite WGCNA withr xfun xml2 XVector yaml zoo

gDRplots

Rendered fromgDRplots.Rmdusingknitr::rmarkdown

Last update: 2026-07-01
Started: 2026-06-11

Help page	Topics
Analyze Chemical Genomics (CGS) Data and Perform GSEA	analyze_cgs
Compute distance between rows of a matrix.	compute_distances
create a log-sequence	create_log_seq
Create a nested list of plots for PRISM data with combo metrics	create_PRISM_plot_list_combo
Create a nested list of plots for PRISM data with single-agent metrics	create_PRISM_plot_list_sa
Create a list of PRISM association table	create_PRISM_summary_list
Fill missing values in the color map for annotation	fill_ann_color_map
Create color map for annotation	get_ann_color_map
Calculate the luminance of a color	get_col_luminance
Get Legend Title	get_hm_title
get_iso_colors	get_iso_colors
Create list of qualitative colors	get_qual_colors
Plot heatmaps of fitted values for combination metrics data	heatmap_combo_metrics
Plot panel of heatmaps of fitted values for combination metrics data	heatmap_combo_metrics_panel
Plot heatmaps of averaged values for combination data	heatmap_combo_with_isoref
Plot panel of heatmaps with fitted and reference data for isobolograms	heatmap_combo_with_isoref_panel
#' Plot panel of heatmaps with fitted and reference data for isobolograms	heatmap_combo_with_isoref_panel_common
Plot panel of heatmaps with fitted and reference data for isobolograms	heatmap_combo_with_isoref_panel_independent
Plot heatmap of mapping controls to treated for single-agent and combo data to control quality of the data	heatmap_control_mapping_qc
Determine whether or not a color is dark	is_color_dark
Determine whether or not a color name is valid	is_valid_color
Plot pretty heatmap for single-agent or combo data to control quality of the data	pheatmap_qc
Plot pretty heatmap with annotations for co-dilution data	pheatmap_with_anno_cd
Plot pretty heatmap with annotations for combo data	pheatmap_with_anno_combo
Plot heatmap with annotations for combo metrics data	pheatmap_with_anno_combo_metrics
Plot pretty heatmap with annotations for single-agent data	pheatmap_with_anno_sa
Plot boxplot for metric values grouped by metadata from DepMap	plot_boxplot_meta
Plot box plots for metric for combo data grouped by selected variable	plot_boxplot_metric_combo
Plot box plots for metric for combo data grouped by cell line names	plot_boxplot_metric_combo_by_CLs
Plot box plots for metric for combo data grouped by drug names	plot_boxplot_metric_combo_by_drugs
Plot box plots for metric for combo data grouped by selected variable	plot_boxplot_metric_combo_by_grp
Plot box plots for metric for single-agent data grouped by selected variable	plot_boxplot_metric_sa
Plot box plots for metric for single-agent data grouped by cell line names	plot_boxplot_metric_sa_by_CLs
Plot box plots for metric for single-agent data grouped by drug names	plot_boxplot_metric_sa_by_drugs
Plot box plots for metric for single-agent data grouped by selected variable	plot_boxplot_metric_sa_by_grp
Plot boxplot for categorical features	plot_boxplot_num
Plot panel with boxplots	plot_boxplot_num_panel
Plot Chemical Genomics Screen GSEA Results	plot_cgs_ranking
Plot line plot of combination index	plot_combination_index
Plot drug response curves for combo data	plot_dose_response_combo
Plot panel with drug response curves for single-agent data to control quality of the data	plot_dose_response_combo_panel
Plot drug response curves for single-agent data	plot_dose_response_sa
Plot drug response curves for single-agent data for selected call lines and drugs	plot_dose_response_sa_by_CLs
Plot drug response curves for single-agent data for selected call lines and drugs	plot_dose_response_sa_by_drugs
Plot drug response curves for single-agent data to control quality of the data	plot_dose_response_sa_qc
Plot panel with drug response curves for single-agent data to control quality of the data	plot_dose_response_sa_qc_panel
Visualization for the quality control of the fitting for single-agent data	plot_fitting_acc
Plot data from a specific column	plot_plate
Plot plate data (Heatmap + Dose Ranks + Smart Legend + Explicit QC)	plot_plate_stack_info
Plot scatter with correlation	plot_scatter_with_corr
Plot panel with scatter with correlation	plot_scatter_with_corr_panel
Plot a single plate's stack info	plot_single_plate_stack_info
Plot a violin plot for normalized or averaged data (single-agent and combo) to control the quality of the data	plot_var_distribution_qc
Lollipop plot for metric single-agent data to control quality of the data	plot_var_stat_qc
Volcano plot with association	plot_volcano_assoc
Plot panel with volcano plot and according to the data type - scatter plots or box plots	plot_volcano_assoc_panel
Prep table with calculated linear associations	prep_dt_assoc
Prep table with metric values by doses for single-agent experiment	prep_dt_response_dose_sa
Prep table with metric values for combination experiment	prep_dt_response_metric_diff
Prep table with metric values for single-agent experiment	prep_dt_response_metric_sa
Prep table with metric values for combination experiment	prep_dt_response_scores
Prep matrix with metric value based on the Metrics assay	prep_pheatmap_matrix
Round numbers to unique string	round_to_unique_string

Package: gDRplots 0.99.3

gDRplots: 'gDRplots'

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