volc_plot: Generate a volcano plot from a data frame containing a gene...

In nodrogluap/gumshoe: Supplemental Statistical Tests and Utilities for Kallisto/Sleuth RNASeq Analysis

Generate a volcano plot from a data frame containing a gene name, q-value, and fold change with user-selected cutoffs and title.

Description

Generate a volcano plot from a data frame containing a gene name, q-value, and fold change with user-selected cutoffs and title.

Usage

volc_plot(
  df,
  label_column_name = "external_gene_name",
  x_axis_column_name = "b",
  y_axis_column_name = "qval",
  x_cutoff = 2,
  y_cutoff = -log10(0.05),
  graph_name = "Sample Graph Name"
)

Arguments

df	A data frame or list containing ensemble transcript id's
label_column_name	The column name of the data point labels. The default is external_gene_name, which is the column name from the output of the ensembl_to_id function.
x_axis_column_name	The column name for the intended x-axis values. The default is "b", which is the name of the column corresponding to the FC after Sleuth analysis.
y_axis_column_name	The column name for the intended y-axis values. The default is "qval", which is the name of the column corresponding to the Benjamini-Hochberg multiple testing corrected p-value after Sleuth analysis.
x_cutoff	X-axis cutoff, which corresponds to the fold change. Default value is 2.
y_cutoff	Y-axis cutoff, which corresponds to the q-value. Default value is -log10(.05).
graph_name	Name of the graph. Default is "Sample Graph Name".

Examples

# Create a volcano plot from a data frame with gene symbols, q-value, and FC.
volc_plot(wald_sig_results, graph_name = "Treated v. WT - Sex Factor")

nodrogluap/gumshoe documentation built on Feb. 28, 2023, 6:15 p.m.