make_volcano_plot: Make volcano plot

In gaelfortin/phosphogo: Analyze Your Phosphoproteomic Data

Description

Draw a volcano plot from any test results

Usage

make_volcano_plot(
  kinase_enrichment_file = "kinase_enrichment_networkin.csv",
  odds_ratio = odds_ratio,
  FDR_cutoff = 0.05,
  FDR_data = FDR,
  labels = top_predicted_kinase,
  graph_title = "Volcano plot",
  x_axis_title = "X axis",
  output_folder = "myexperiment/",
  file_name
)

Arguments

kinase_enrichment_file	<character> Name of the file with Fisher exact test results
odds_ratio	<column_name> Unquoted name of the kinase_enrichment_file column that contains the odds ratios.
FDR_cutoff	<numeric> Cutoff to display.
FDR_data	<column_name> Unquoted name of kinase_enrichment_file column that contains the FDR values.
labels	<column_name> Unquoted name of kinase_enrichment_file column that contains the labels.
graph_title	<character>
x_axis_title	<character>
output_folder	<character> Where the output files should be stored
file_name	<character> File name including extension (.pdf recommended)

gaelfortin/phosphogo documentation built on Nov. 26, 2020, 9:12 a.m.