Plot drug response curves for single-agent data

Plot drug response curves for single-agent data

Usage

plot_dose_response_sa(
  dt_metrics,
  dt_average,
  selection_name,
  group_var,
  group_names = NULL,
  normalization_type = "GR",
  colors_vec = NULL,
  plot_averaged_flag = TRUE,
  plot_fit_flag = TRUE,
  fit_source = "gDR"
)

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

dt_average

data.table representing data from the Averaged assay, outputted by gDRutils::convert_se_assay_to_dt(se, "Averaged") and single-agent SummarizedExperiment

selection_name

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

group_var

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

group_names

character vector with names to subset from se (the same dim as 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")

colors_vec

character vector with colors for group_names - name or hex value

plot_averaged_flag

logical flag whether plot points with average values

plot_fit_flag

logical flag whether plot points with fitted values

fit_source

string source name for metrics

Value

ggplot object containing plot of dose-response curves

Note

inspired by the grob_SA function written by Marc Hafner

Examples

mae <- gDRutils::get_synthetic_data("small")
se <- mae[[gDRutils::get_supported_experiments("sa")]]
selected_drug <- "drug_002"
group_var <- "CellLineName"
dt_metrics <- gDRutils::convert_se_assay_to_dt(se, "Metrics")
dt_average <- gDRutils::convert_se_assay_to_dt(se, "Averaged")
celline_names <- unique(dt_metrics[[group_var]])[1:3]

plot_dose_response_sa(dt_metrics = dt_metrics,
                      dt_average = dt_average,
                      selection_name = selected_drug,
                      group_var = group_var,
                      group_names = celline_names)


plot_dose_response_sa(dt_metrics = dt_metrics,
                      dt_average = NULL,
                      selection_name = selected_drug,
                      group_var = group_var,
                      group_names = celline_names)


selected_cellline <- "cellline_HB"
group_var <- "DrugName"
dt_metrics <- gDRutils::convert_se_assay_to_dt(se, "Metrics")
dt_average <- gDRutils::convert_se_assay_to_dt(se, "Averaged")
group_names <- unique(dt_metrics[[group_var]])[1:3]

plot_dose_response_sa(dt_metrics = dt_metrics,
                      dt_average = dt_average,
                      selection_name = selected_cellline,
                      group_var = group_var,
                      group_names = group_names)