Plot panel of heatmaps with fitted and reference data for isobolograms

Plot panel of heatmaps with fitted and reference data for isobolograms

Usage

heatmap_combo_with_isoref_panel(
  dt_excess,
  dt_isobolograms,
  drug1_name,
  drug2_name,
  cl_names,
  normalization_type = "GR",
  metric = "smooth",
  iso_levels = "0.5",
  colors_vec = NULL,
  no_breaks = 50,
  swap_axes = FALSE
)

Arguments

dt_excess

data.table representing data from the excess assay, outputted by gDRutils::convert_se_assay_to_dt(se, "excess") and combo SummarizedExperiment

dt_isobolograms

data.table representing data from the isobolograms assay, outputted by gDRutils::convert_se_assay_to_dt(se, "isobolograms") and combo SummarizedExperiment

drug1_name

string with drug name to be plotted (identifiers DrugName)

drug2_name

string with co-drug name to be plotted (identifiers DrugName_2)

cl_names

character vector with cell line names to be plotted (Cell Line Name); if NULL - all available cell lines will be plotted

normalization_type

string with normalization_types to be selected one of: "GR" ("GRvalue") or "RV" ("RelativeViability")

metric

string name of the combo metric; one of: "smooth" ("Smooth GR" or "Smooth RV" - respectively depending on normalization_type) "hsa_excess" ("Bliss Excess GR" or "Bliss Excess RV") or "bliss_excess" ("Bliss Excess GR" or "Bliss Excess RV")

iso_levels

character vector with isobologram levels to be selected; when NULL - no isolines will be displayed

colors_vec

character vector of colors (valid name or hex) used in heatmap; the default depends on metric: for "smooth" - the dark purple-light grey palette and for "hsa_excess" and "bliss_excess" - the blue-light grey-red color scale

no_breaks

numeric number of breaks on scale

swap_axes

logical flag whether to swap the axes with drugs of the heatmap

Value

ggplot object containing panel with heatmaps for fitted values and reference data for isobolograms for selected drug and co-drug and all selected cell line

Examples

cl_names <-
  c("cellline_AA", "cellline_EA", "cellline_IB",
  "cellline_MC", "cellline_BC", "cellline_FD")

drug1_name <- "drug_001"
drug2_name <- "drug_026"

mae <- gDRutils::get_synthetic_data("combo_matrix")
se <- mae[[gDRutils::get_supported_experiments("combo")]]
dt_excess <- gDRutils::convert_se_assay_to_dt(se, "excess")
dt_isobolograms <- gDRutils::convert_se_assay_to_dt(se, "isobolograms")

heatmap_combo_with_isoref_panel(dt_excess,
                                dt_isobolograms,
                                drug1_name, drug2_name,
                                cl_names)


dt_excess_2 <- data.table::copy(dt_excess)
invisible(dt_excess_2[CellLineName %in% cl_names[1:2],
                      Concentration := Concentration / 10])

heatmap_combo_with_isoref_panel(dt_excess_2,
                                dt_isobolograms,
                                drug1_name, drug2_name,
                                cl_names,
                                iso_levels = c("0.25", "0.75"),
                                colors_vec = c("darkcyan", "snow", "coral"))