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Create a list of PRISM plots for a selected type of experiment

Source: R/helpers-prism-plotlist.R
dot-create_PRISM_plot_list.Rd

This internal function was created to avoid code duplication and maintain consistency. For user, it is contained in a single-purpose function, depending on the experiment type.

Usage

.create_PRISM_plot_list(
  experiment_type,
  dt_metrics_sa,
  dt_metrics_combo = NULL,
  dt_average = NULL,
  dt_scores = NULL,
  drug1_name_vec = NULL,
  drug2_name_vec = NULL,
  normalization_type_vec = "RV",
  metric = c("xc50", "x_mean", "x_max"),
  metric_scores = c("hsa_score", "bliss_score"),
  fit_source = "gDR",
  meta_data_path,
  feat_data_path,
  feature_sets,
  metadata_columns = NULL,
  clear_taxonomy_info = TRUE,
  with_decoding = FALSE
)

Arguments

experiment_type

string with the type of experiment one of: "sa" for the single-agent experiment "combo" for the combination experiment

dt_metrics_sa

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

dt_metrics_combo

data.table representing data from the Metrics assay, outputted by gDRutils::convert_se_assay_to_dt(se, "Metrics") and combo 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

dt_scores

data.table representing data from the scores assay, outputted by gDRutils::convert_se_assay_to_dt(se, "scores") and combo SummarizedExperiment

drug1_name_vec

character vector with drug names to be plotted (identifiers DrugName)

drug2_name_vec

character vector with co-drug names to be plotted (identifiers DrugName_2)

normalization_type_vec

character vector with normalization types to be selected one of: "GR" ("GRvalue") or "RV" ("RelativeViability") or both

metric

character vector with names of metric; chosen from: "xc50" ("GR50" or "IC50" - respectively depending on normalization_type), "x_max" ("GR Max" or "E Max") or "x_mean" ("GR Mean" or "RV Mean")

metric_scores

character vector with names of combo metric; chosen from: "hsa_score"("Bliss Excess GR" or "Bliss Excess RV" - respectively depending on normalization_type), "bliss_score" ("Bliss Score GR" or "Bliss Score RV")

fit_source

string source name for metrics

meta_data_path

string path to metadata file describing all cancer models/cell lines which are referenced by a dataset contained within the DepMap portal. It is usually a file named Model.csv or Model.csv.gz.

feat_data_path

string path to the directory containing the molecular feature set file to load from DepMap.

feature_sets

character vector containing the names of the molecular feature sets to load from DepMap. These names should also correspond to the file names containing the feature data (without the extension, which is assumed to be csv or csv.gz)

metadata_columns

character vector with the metadata columns to load for DepMap cell lines

clear_taxonomy_info

logical flag whether to remove taxonomy information for gene names in table with the molecular feature sets from DepMap.

with_decoding

logical whether the feature OmicsArmLevelCNA, OmicsSomaticMutationsMatrixHotspot and OmicsSomaticMutationsMatrixDamaging should be encoded into a 0-1 scheme

Value

A named list with elements:

  • ls_plot nested list of plots for selected type of experiment

  • ls_assoc_data nested list of table with association data

Author

Janina Smoła janina.smola@external.roche.com