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

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

Usage

plot_boxplot_metric_combo_by_grp(
  dt_scores,
  selection_var,
  selection_name,
  group_var,
  group_names = NULL,
  normalization_type = "GR",
  metric = "hsa_score",
  fit_source = "gDR",
  named_n = 5,
  named_n_mode = "top",
  grouped_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

selection_var

string name of selected main variable - one value from column "CellLineName" or "DrugName"

selection_name

string name of selected variable value from column selection_var to filter data for plotting

group_var

string name of group variable; should to be not numeric variable from dt_metrics different than selection_var and not containing unique values for each row

group_names

character vector with names to subset from column group_var; if NULL then all values 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: "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

named_n

number of points to label based on the highest or lowest metric values; if group_var is "DrugName", points are labeled by "CellLineName" and similarly vice versa

named_n_mode

string determines whether the labels are applied to the highest or lowest values of metric; one of: "top" or "bottom"

grouped_flag

logical flag whether the boxplots should be colored by group_var

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 selected variable

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")
invisible(dt_scores[, Tissue_grp := data.table::fifelse(Tissue == "tissue_w",
                                                        "tissue_w",
                                                        "tissue_other")])

plot_boxplot_metric_combo_by_grp(dt_scores,
                                 selection_var = "DrugName",
                                 selection_name = c("drug_001", "drug_021"),
                                 group_var = "Tissue")


plot_boxplot_metric_combo_by_grp(dt_scores,
                                 selection_var = "DrugName",
                                 selection_name = c("drug_001", "drug_021"),
                                 group_var = "Tissue_grp",
                                 grouped_flag = TRUE,
                                 colors_vec = c("darkblue", "deeppink"))


plot_boxplot_metric_combo_by_grp(dt_scores,
                                 selection_var = "DrugName",
                                 selection_name = c("drug_001", "drug_021"),
                                 group_var = "Tissue",
                                 grouped_flag = TRUE)


plot_boxplot_metric_combo_by_grp(dt_scores,
                                 selection_var = "DrugName",
                                 selection_name = c("drug_001", "drug_021"),
                                 group_var = "Tissue",
                                 colors_vec = c("darkblue", "orange"))