glMDPlot.DGELRT: Glimma MD Plot

In Shians/Glimma: Interactive HTML graphics

Glimma MD Plot

Description

Draw an interactive MD plot from a DGELRT object

Usage

## S3 method for class 'DGELRT'
glMDPlot(
  x,
  counts = NULL,
  anno = NULL,
  groups = NULL,
  samples = NULL,
  status = rep(0, nrow(x)),
  transform = FALSE,
  main = "",
  xlab = "Average log CPM",
  ylab = "log-fold-change",
  side.xlab = "Group",
  side.ylab = "Expression",
  side.log = FALSE,
  side.gridstep = ifelse(!transform || side.log, FALSE, 0.5),
  p.adj.method = "BH",
  jitter = 30,
  side.main = "GeneID",
  display.columns = NULL,
  cols = c("#00bfff", "#858585", "#ff3030"),
  sample.cols = rep("#1f77b4", ncol(counts)),
  path = getwd(),
  folder = "glimma-plots",
  html = "MD-Plot",
  launch = TRUE,
  ...
)

Arguments

x	the DGELRT object.
counts	the matrix of expression values, with samples in columns.
anno	the data.frame containing gene annotations.
groups	the factor containing experimental groups of the samples.
samples	the names of the samples.
status	vector giving the control status of data point, of same length as the number of rows of object. If NULL, then all points are plotted in the default colour.
transform	TRUE if counts should be log-cpm transformed.
main	the title for the left plot.
xlab	label for x axis on left plot.
ylab	label for y axis on left plot.
side.xlab	label for x axis on right plot.
side.ylab	label for y axis on right plot.
side.log	TRUE to plot expression on the right plot on log scale.
side.gridstep	intervals along which to place grid lines on y axis. Currently only available for linear scale.
p.adj.method	character vector indicating multiple testing correction method. See p.adjust for available methods. (defaults to "BH")
jitter	the amount of jitter to apply to the samples in the expressions plot.
side.main	the column containing mains for right plot.
display.columns	character vector containing names of columns to display in mouseover tooltips and table.
cols	vector of strings denoting colours corresponding to control status -1, 0 and 1. (may be R named colours or Hex values)
sample.cols	vector of strings denoting colours for each sample point on the expression plot.
path	the path in which the folder will be created.
folder	the name of the fold to save html file to.
html	the name of the html file to save plots to.
launch	TRUE to launch plot after call.
...	additional arguments to be passed onto the MD plot. (main, xlab, ylab can be set for the left plot)

Value

Draws a two-panel interactive MD plot in an html page. The left plot shows the log-fold-change vs average expression. The right plot shows the expression levels of a particular gene of each sample. Hovering over points on left plot will plot expression level for corresponding gene, clicking on points will fix the expression plot to gene. Clicking on rows on the table has the same effect as clicking on the corresponding gene in the plot.

Author(s)

Shian Su

Shians/Glimma documentation built on Sept. 7, 2024, 4:25 p.m.