glMDPlot.DGELRT: Glimma MD Plot

Description Usage Arguments Value Author(s)

View source: R/glMDPlot.R

Description

Draw an interactive MD plot from a DGELRT object

Usage

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## 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


Glimma documentation built on April 29, 2020, 5:38 a.m.