subVolcano: volcano plot

In peterawe/CMScaller: CMScaller: an R package for consensus molecular subtyping of colorectal cancer pre-clinical models

Description

Volcano plot of output from subDEG.

Usage

subVolcano(
  deg,
  geneID = "rownames",
  lfc = log2(2),
  padj = 0.05,
  ave = 0,
  topN = 10,
  cexText = 1,
  classCol = getOption("subClassCol"),
  ...
)

Arguments

deg	output from subDEG which may be either a list or a data frame.
geneID	deg column name to use for labeling top hits.
lfc	a numeric absolute log2(fold-change) threshold.
padj	a numeric, adjusted p-value threshold. length(class)==ncol(emat).
ave	a numeric, average expression threshold.
topN	an integer, number of genes to label in plot (selected by largest absolute fold-change).
cexText	a numeric, scaling factor for labels for top hits.
classCol	a character vector specifying class colors.
...	additional arguments passed to plot or smoothScatter or if KernSmooth is available (currently only main, xlab and ylab used).

Value

one or more volcano plots where horizontal dashed line is the maximum p-value below padj and vertical lines the lfc-threshold.

peterawe/CMScaller documentation built on June 13, 2020, 4:49 a.m.