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(
  dt_metrics,
  group_var,
  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

group_var

string name of group variable; one of: "CellLineName" or "DrugName"

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 group_var

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(dt_metrics,
                       group_var = "CellLineName")


plot_boxplot_metric_sa(dt_metrics,
                       group_var = "DrugName")


plot_boxplot_metric_sa(dt_metrics,
                       group_var = "DrugName",
                       metric = "x_AOC_range",
                       colors_vec = "grey",
                       colored_pts_flag = TRUE)


plot_boxplot_metric_sa(dt_metrics,
                       group_var = "CellLineName",
                       normalization_type = "RV",
                       metric = "x_max",
                       colors_vec = c("gold", "darkorange", "darkcyan", "darkblue"),
                       grouped_flag = TRUE)