vulcan: Vulcan: Generate easy volcano plots from sleuth results test...

In genejockey33000/typGumbo: Scripts and Pipelines for RNAseq Analysis

Vulcan: Generate easy volcano plots from sleuth results test tables

Description

Takes the output of sleuth_results() and generates a volcano plot with relative ease and includes a few key adjustable parameters. Test table is trimmed of all rows with NAs (retained in sleuth_results()). ENSGs without mapped ext_gene names are also trimmed.

Usage

vulcan(
  x,
  bcut = 0.5,
  qcut = 0.05,
  labels = 0,
  repel = 1,
  pad = 0.25,
  labelsize = 4
)

Arguments

x	Output from sleuth_results() or any test tables with values for b and for qval
bcut	Cutoff value for b (log fold change) for significance
qcut	Cutoff value for qval (adjusted pval) for significance
labels	How many of the top DEG data points to label. Top DEGs are identified buy calculating the rank = -lot10(qval) * bval. Vulcan will plots the top and bottom scores. Default is 0 and prints no labels.
repel	Force of point label repulsion (from geom_text_repel()). Default = 1
pad	Padding around label boxes (from geom_text_repel()). Default = 0.25
labelsize	Size of labels (from geom_text_repel()). Default = 4

Value

volcano plot

genejockey33000/typGumbo documentation built on July 20, 2023, 11:45 p.m.