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Plot box plots for metric for combo data grouped by selected variable

Source: R/plot-boxplot_metric.R
plot_boxplot_metric_combo.Rd

Plot box plots for metric for combo data grouped by selected variable

Usage

plot_boxplot_metric_combo(
  dt_scores,
  group_var,
  normalization_type = "GR",
  metric = "hsa_score",
  fit_source = "gDR",
  grouped_flag = FALSE,
  colored_pts_flag = FALSE,
  colors_vec = NULL
)

Arguments

dt_scores

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

group_var

string name of group variable; one of: "CellLineName" or "DrugName"; for group_var set as "DrugName" points will be grouped by drug combinations "DrugName" x "DrugName_2"

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: "hsa_score"("Bliss Excess GR" or "Bliss Excess RV" - respectively depending on normalization_type) or "bliss_score" ("Bliss Score GR" or "Bliss Score RV")

fit_source

string source name for metrics

grouped_flag

a logical flag whether the boxplots should be grouped and colored by Tissue for group_var set as "CellLineName" and drug_moa - for "DrugName"

colored_pts_flag

a logical flag whether the points should be colored by grouped variable - for group_var equal "CellLineName" points will be colored by "DrugName" and similarly vice versa

colors_vec

character vector with colors (name or hex value) to color boxplots; for grouped_flag set as FALSE only first from vector will be used

Value

ggplot object containing boxplots for selected combo metric grouped by group_var

Author

Janina Smoła janina.smola@external.roche.com

Examples

mae <- gDRutils::get_synthetic_data("combo_matrix")
se <- mae[[gDRutils::get_supported_experiments("combo")]]

dt_scores <- gDRutils::convert_se_assay_to_dt(se = se,
                                              assay_name = "scores")

plot_boxplot_metric_combo(dt_scores,
                          group_var = "DrugName")


plot_boxplot_metric_combo(dt_scores,
                          group_var = "DrugName",
                          colored_pts_flag = TRUE,
                          colors_vec = "grey")


plot_boxplot_metric_combo(dt_scores,
                          group_var = "CellLineName",
                          metric = "hsa_score",
                          normalization_type = "RV",
                          grouped_flag = TRUE)


plot_boxplot_metric_combo(
  dt_scores,
  group_var = "CellLineName",
  metric = "hsa_score",
  grouped_flag = TRUE,
  colors_vec = c("deeppink", "darkblue"))