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Plot heatmaps of averaged values for combination data

Source: R/plot-combo-heatmaps.R
heatmap_combo_with_isoref.Rd

Plot heatmaps of averaged values for combination data

Usage

heatmap_combo_with_isoref(
  dt_excess,
  dt_isobolograms,
  drug1_name,
  drug2_name,
  cl_name,
  normalization_type = "GR",
  metric = "smooth",
  iso_levels = "0.5",
  colors_vec = NULL,
  colors_vec_iso = 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_name

string with cell line to be plotted (identifiers CellLineName)

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

colors_vec_iso

character vector of colors (valid name or hex) used for the isolines; the default is the dark red-orange palette

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 heatmap for fitted values and reference data for isobolograms for selected drug and co-drug and selected cell line

Examples

cl_name <- "cellline_BC"
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(dt_excess,
                          dt_isobolograms,
                          drug1_name, drug2_name,
                          cl_name)


heatmap_combo_with_isoref(dt_excess,
                          dt_isobolograms,
                          drug1_name, drug2_name,
                          cl_name,
                          metric = "hsa_excess",
                          iso_levels = c("-0.2", "0.2"))


heatmap_combo_with_isoref(dt_excess,
                          dt_isobolograms,
                          drug1_name, drug2_name,
                          cl_name,
                          iso_levels = NULL,
                          colors_vec = c("darkcyan", "snow", "darkorange"))


heatmap_combo_with_isoref(dt_excess,
                          dt_isobolograms,
                          drug1_name, drug2_name,
                          cl_name,
                          normalization_type = "RV",
                          iso_levels = c("0.25", "0.75"),
                          swap_axes = FALSE)


heatmap_combo_with_isoref(dt_excess,
                          dt_isobolograms,
                          drug1_name, drug2_name,
                          cl_name,
                          normalization_type = "RV",
                          iso_levels = c("0.25", "0.75"),
                          swap_axes = TRUE)


heatmap_combo_with_isoref(dt_excess,
                          dt_isobolograms,
                          drug1_name, drug2_name,
                          cl_name,
                          metric = "hsa_excess",
                          iso_levels = c("0.25", "0.75"),
                          colors_vec_iso = c("0.25" = "darkcyan",
                                             "0.75" = "darkblue"),
                          swap_axes = FALSE)