Plot a violin plot for normalized or averaged data (single-agent and combo) to control the quality of the data

Plot a violin plot for normalized or averaged data (single-agent and combo) to control the quality of the data

Usage

plot_var_distribution_qc(
  dt_assay,
  cl_name,
  metric = "x",
  normalization_type = "GR"
)

Arguments

dt_assay

data.table representing data from the assay, outputted by gDRutils::convert_se_assay_to_dt(se, <assay_name>) for assay_name like Normalized or Averaged and SummarizedExperiment with chosen data type: single-agent or combo

cl_name

string cell line name to be plotted (Cell Line Name)

metric

string with variable name to be plotted; it has to be in dt_assay

normalization_type

string with normalization_types to be selected one of: "GR" ("GRvalue") or "RV" ("RelativeViability")

Value

ggplot object containing plot with violin for each drug

Examples

mae <- gDRutils::get_synthetic_data("combo_matrix")
se <- mae[[gDRutils::get_supported_experiments("sa")]]

dt_norm <- gDRutils::convert_se_assay_to_dt(se, "Normalized")
cl_name <- dt_norm[["CellLineName"]][1]

plot_var_distribution_qc(dt_assay = dt_norm,
                         cl_name = cl_name)


dt_average <- gDRutils::convert_se_assay_to_dt(se, "Averaged")
plot_var_distribution_qc(dt_assay = dt_average,
                         cl_name = cl_name,
                         normalization_type = "RV")


plot_var_distribution_qc(dt_assay = dt_average,
                         cl_name = cl_name,
                         metric = "x_std",
                         normalization_type = "RV")


mae <- gDRutils::get_synthetic_data("combo_matrix")
se <- mae[[gDRutils::get_supported_experiments("combo")]]

dt_norm <- gDRutils::convert_se_assay_to_dt(se, "Normalized")
cl_name <- dt_norm[["CellLineName"]][1]

plot_var_distribution_qc(dt_assay = dt_norm,
                         cl_name = cl_name)


dt_average <- gDRutils::convert_se_assay_to_dt(se, "Averaged")
plot_var_distribution_qc(dt_assay = dt_average,
                         cl_name = cl_name,
                         normalization_type = "RV")