maplot: Plots MA plot for the Hodges lab

In hodgeslab/hodgeslabR: Common Code for the Hodges Lab

Description

This function reads a data frame either directly from the results output of DESeq2, or by importing a table saved directly from such a result data frame.

Usage

maplot(
  res,
  foldthresh = log2(1.5),
  pthresh = 0.1,
  colpal_unch = "greys",
  colpal_incr = "oranges",
  colpal_decr = "blues",
  minCount = 0,
  ylim = c(-2.25, 2.25),
  label = F,
  maxlabel = 50,
  grid = F,
  box = T,
  ...
)

Arguments

res	Results data frame from DESeq2. Important fields are "id", "baseMean", "log2FoldChange", "padj", and "label".
foldthresh	Threshold for calling changes in either direction based on fold change. Defaults to log2(1.5).
pthresh	Threshold for calling changes in either direction based on padj. Defaults to 0.10.
colpal_unch	Color palette for unchanged sites, options from LSD::disco(). Defaults to "greys".
colpal_incr	Color palette for increased sites, options from LSD::disco(). Defaults to "oranges".
colpal_decr	Color palette for decreased sites, options from LSD::disco(). Defaults to "blues".
minCount	Minimum x value to plot. Defaults to 0.
ylim	Two-element vector setting the y-axis limits. Defaults to c(-2.25,2.25).
label	Variable describing how or if labeling should occur. Can be TRUE, FALSE, or "auto". Defaults to FALSE.
maxlabel	Indicates maximum number of labels to place on the plot. Only is evaluated when label == TRUE. Defaults to 50.
grid	Boolean describing whether to show major gridlines. Defaults to FALSE.
box	Boolean describing whether to place a box around the plot area. Defaults to TRUE.

Examples

maplot(res)

hodgeslab/hodgeslabR documentation built on Aug. 6, 2021, 5:10 a.m.