Plot box plots for metric for single-agent data grouped by selected variable

Plot box plots for metric for single-agent data grouped by selected variable

Usage

plot_boxplot_metric_sa_by_grp(
  dt_metrics,
  selection_var,
  selection_name,
  group_var,
  group_names = NULL,
  normalization_type = "GR",
  metric = "xc50",
  fit_source = "gDR",
  named_n = 5,
  named_n_mode = "bottom",
  grouped_flag = FALSE,
  colors_vec = NULL,
  with_inf = FALSE
)

Arguments

dt_metrics

data.table representing data from the Metrics assay, outputted by gDRutils::convert_se_assay_to_dt(se, "Metrics") and single-agent 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 metric; one of: "xc50" ("GR50" or "IC50" - respectively depending on normalization_type), "x_max" ("GR Max" or "E Max") or "x_mean" ("GR Mean" or "RV Mean"), but the values from any numeric column can be displayed

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

with_inf

a logical flag indicating whether infinite values should be shown on boxplots

Value

ggplot object containing boxplots for selected single-agent 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("sa")]]

dt_metrics <- gDRutils::convert_se_assay_to_dt(se, "Metrics")
invisible(dt_metrics[, Tissue_grp := data.table::fifelse(Tissue == "tissue_w",
                                                         "tissue_w",
                                                         "tissue_other")])

plot_boxplot_metric_sa_by_grp(dt_metrics,
                              selection_var = "DrugName",
                              selection_name = "drug_001",
                              group_var = "Tissue")


plot_boxplot_metric_sa_by_grp(dt_metrics,
                              selection_var = "DrugName",
                              selection_name = "drug_001",
                              group_var = "Tissue_grp")


plot_boxplot_metric_sa_by_grp(dt_metrics,
                              selection_var = "DrugName",
                              selection_name = "drug_001",
                              group_var = "Tissue",
                              with_inf = TRUE)


plot_boxplot_metric_sa_by_grp(dt_metrics,
                              selection_var = "DrugName",
                              selection_name = "drug_001",
                              group_var = "Tissue",
                              named_n = 0)


plot_boxplot_metric_sa_by_grp(dt_metrics,
                              selection_var = "DrugName",
                              selection_name = "drug_001",
                              group_var = "Tissue",
                              grouped_flag = TRUE)


plot_boxplot_metric_sa_by_grp(dt_metrics,
                              selection_var = "DrugName",
                              selection_name = "drug_001",
                              group_var = "Tissue",
                              colors_vec = c("darkblue", "deeppink"))