subVolcano: volcano plot

Description Usage Arguments Value

View source: R/subVolcano.R

Description

Volcano plot of output from subDEG.

Usage

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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.