Package index • gDRplots

Single-agent plots

Function to plot drug response curves for single-agent data

plot_boxplot_metric_sa(): Plot box plots for metric for single-agent data grouped by selected variable
plot_boxplot_metric_sa_by_CLs(): Plot box plots for metric for single-agent data grouped by cell line names
plot_boxplot_metric_sa_by_drugs(): Plot box plots for metric for single-agent data grouped by drug names
plot_boxplot_metric_sa_by_grp(): Plot box plots for metric for single-agent data grouped by selected variable
plot_dose_response_sa(): Plot drug response curves for single-agent data
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 for selected call lines and drugs

Function to plot averaged values heatmaps for combo data

heatmap_combo_metrics(): Plot heatmaps of fitted values for combination metrics data
heatmap_combo_metrics_panel(): Plot panel of heatmaps of fitted values for combination metrics data
heatmap_combo_with_isoref(): Plot heatmaps of averaged values for combination data
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 panel of heatmaps with fitted and reference data for isobolograms
plot_boxplot_metric_combo(): Plot box plots for metric for combo data grouped by selected variable
plot_boxplot_metric_combo_by_CLs(): Plot box plots for metric for combo data grouped by cell line names
plot_boxplot_metric_combo_by_drugs(): Plot box plots for metric for combo data grouped by drug names
plot_boxplot_metric_combo_by_grp(): Plot box plots for metric for combo data grouped by selected variable
plot_combination_index(): Plot line plot of combination index
plot_dose_response_combo(): Plot drug response curves for combo data
plot_dose_response_combo_panel(): Plot panel with drug response curves for single-agent data to control quality of the data

QC plots for Processing Report with all helpers

heatmap_control_mapping_qc(): Plot heatmap of mapping controls to treated for single-agent and combo data to control quality of the data
pheatmap_qc(): Plot pretty heatmap for single-agent or combo data to control quality of the data
plot_dose_response_sa_qc(): Plot drug response curves for single-agent data to control quality of the data
plot_dose_response_sa_qc_panel(): Plot panel with drug response curves for single-agent data to control quality of the data
plot_fitting_acc(): Visualization for the quality control of the fitting for single-agent data
plot_plate(): Plot data from a specific column
plot_plate_stack_info(): Plot plate data (Heatmap + Dose Ranks + Smart Legend + Explicit QC)
plot_single_plate_stack_info(): Plot a single plate's stack info
plot_var_distribution_qc(): Plot a violin plot for normalized or averaged data (single-agent and combo) to control the quality of the data
plot_var_stat_qc(): Lollipop plot for metric single-agent data to control quality of the data

Functions to plot annotated heatmap with helpers

get_hm_title(): Get Legend Title
pheatmap_with_anno_cd(): Plot pretty heatmap with annotations for co-dilution data
pheatmap_with_anno_combo(): Plot pretty heatmap with annotations for combo data
pheatmap_with_anno_combo_metrics(): Plot heatmap with annotations for combo metrics data
pheatmap_with_anno_sa(): Plot pretty heatmap with annotations for single-agent data
prep_pheatmap_matrix(): Prep matrix with metric value based on the Metrics assay

Functions to plot PRISM visualisation with helpers

create_PRISM_plot_list_combo(): Create a nested list of plots for PRISM data with combo metrics
create_PRISM_plot_list_sa(): Create a nested list of plots for PRISM data with single-agent metrics
create_PRISM_summary_list(): Create a list of PRISM association table
.create_PRISM_plot_list(): Create a list of PRISM plots for a selected type of experiment
.get_data_type(): Check data type
.get_n_top_asssoc(): Get n-top linear associations
plot_boxplot_meta(): Plot boxplot for metric values grouped by metadata from DepMap
plot_boxplot_num(): Plot boxplot for categorical features
plot_boxplot_num_panel(): Plot panel with boxplots
plot_scatter_with_corr(): Plot scatter with correlation
plot_scatter_with_corr_panel(): Plot panel with scatter with correlation
plot_volcano_assoc(): Volcano plot with association
plot_volcano_assoc_panel(): Plot panel with volcano plot and according to the data type - scatter plots or box plots
prep_dt_assoc(): Prep table with calculated linear associations
prep_dt_response_dose_sa(): Prep table with metric values by doses for single-agent experiment
prep_dt_response_metric_diff(): Prep table with metric values for combination experiment
prep_dt_response_metric_sa(): Prep table with metric values for single-agent experiment
prep_dt_response_scores(): Prep table with metric values for combination experiment

Plot color helpers

Utils function

Functions to plot chemical genomics visualisation with helpers