Skip to contents

Plot Chemical Genomics Screen GSEA Results

Source: R/plot-chemical_genomics.R
plot_cgs_ranking.Rd

Generates a ggplot2 visualization of chemical genomics screening data, highlighting GSEA results.

Usage

plot_cgs_ranking(
  results,
  cl_name,
  metric,
  padj_threshold = 0.1,
  top_results_no_sig = 5,
  max_results_with_sig = 15
)

Arguments

results

A list object returned from `analyze_cgs`.

cl_name

A string specifying the cell line included in the results to prepare a visualization.

metric

A string specifying the metric included in the results to prepare a visualization.

padj_threshold

A numeric value specifying the threshold for filtering significant GSEA results based on adjusted p-value.

top_results_no_sig

A numeric value specifying the number of top results to plot if there are no significant values.

max_results_with_sig

A numeric value specifying the maximum number of results to plot when there are more than this number of significant values.

Value

A ggplot2 object with cgs results

Author

Bartosz Czech czech.bartosz@external.gene.com

Examples

dt_metrics <- qs2::qs_read(system.file("testdata/cgs_data.qs2", package = "gDRplots"))
results <- analyze_cgs(dt_metrics, metrics = c("xc50"), cl_name = "CellLineName_1")
#> In `dt_metrics` some xc50 values are infinite.
plot_cgs_ranking(results,
  cl_name = "CellLineName_1",
  metric = "xc50",
  padj_threshold = 0.1,
  top_results_no_sig = 5,
  max_results_with_sig = 15)