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Plot box plots for metric for single-agent data grouped by cell line names

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

Plot box plots for metric for single-agent data grouped by cell line names

Usage

plot_boxplot_metric_sa_by_CLs(
  dt_metrics,
  normalization_type = "GR",
  metric = "xc50",
  fit_source = "gDR",
  grouped_flag = FALSE,
  colored_pts_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

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

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

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 cellline names

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")

plot_boxplot_metric_sa_by_CLs(dt_metrics)


plot_boxplot_metric_sa_by_CLs(dt_metrics,
                              grouped_flag = TRUE)


plot_boxplot_metric_sa_by_CLs(dt_metrics,
                              with_inf = TRUE)


plot_boxplot_metric_sa_by_CLs(dt_metrics,
                              metric = "x_AOC",
                              colors_vec = "gold")


plot_boxplot_metric_sa_by_CLs(
  dt_metrics,
  metric = "x_max",
  colored_pts_flag = TRUE)


plot_boxplot_metric_sa_by_CLs(
  dt_metrics,
  metric = "x_mean",
  grouped_flag = TRUE,
  colors_vec = c("deeppink", "darkcyan", "orange", "darkblue"))