Plot heatmaps of fitted values for combination metrics data

Usage

heatmap_combo_metrics(
  dt_excess,
  dt_isobolograms = NULL,
  drug1_name,
  drug2_name,
  cl_name,
  metric = "smooth",
  normalization_type = "GR",
  iso_levels = c("0.25", "0.5", "0.75"),
  colors_vec_smooth = NULL,
  colors_vec_excess = NULL,
  limit = NULL,
  no_breaks = 50,
  swap_axes = FALSE,
  show_values = 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)
metric: string name of 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")
normalization_type: string with normalization_types to be selected one of: "GR" ("GRvalue") or "RV" ("RelativeViability")
iso_levels: character vector with isobologram levels to be selected
colors_vec_smooth: character vector of colors (valid names or hex codes) used in the heatmap for smooth values; the default is the dark purple-light grey palette
colors_vec_excess: character vector of colors (valid name or hex codes) used in the heatmap for excess values; the default is the blue-light grey-red color scale
limit: numeric vector of length two providing limits of the scale. Use NA to refer to the existing minimum or maximum
no_breaks: numeric number of breaks on scale
swap_axes: logical flag indicating whether to swap the axes with drugs of the heatmap
show_values: logical flag indicating whether to show values of the metric on the heatmap

Value

ggplot object containing heatmap with the values for the selected combo metric for selected drugs and cell line with selected isoline (when chosen)

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_metrics(dt_excess,
                      dt_isobolograms,
                      drug1_name, drug2_name,
                      cl_name,
                      normalization_type = "GR")


heatmap_combo_metrics(dt_excess,
                      dt_isobolograms,
                      drug1_name, drug2_name,
                      cl_name,
                      normalization_type = "GR",
                      swap_axes = TRUE)


heatmap_combo_metrics(dt_excess,
                      dt_isobolograms,
                      drug1_name, drug2_name,
                      cl_name,
                      metric = "hsa_excess",
                      normalization_type = "GR",
                      limit = c(NA, 0.1))


cl_name <- "cellline_JE"
drug1_name <- "drug_011"
drug2_name <- "drug_026"

heatmap_combo_metrics(dt_excess,
                      dt_isobolograms,
                      drug1_name, drug2_name,
                      cl_name,
                      metric = "bliss_excess",
                      normalization_type = "RV",
                      iso_levels = "0.5")


heatmap_combo_metrics(dt_excess,
                      dt_isobolograms,
                      drug1_name, drug2_name,
                      cl_name,
                      metric = "bliss_excess",
                      normalization_type = "RV",
                      iso_levels = NULL)