glMDSPlot.DGEList: Glimma MDS Plot

In Shians/Glimma: Interactive HTML graphics

Description

Glimma MDS Plot

Draw an interactive MD plot from a DGEList object with distances calculated from most variable genes.

Usage

## S3 method for class 'DGEList'
glMDSPlot(
  x,
  top = 500,
  labels = NULL,
  groups = rep(1, ncol(x)),
  gene.selection = c("pairwise", "common"),
  prior.count = 2,
  main = "MDS Plot",
  path = getwd(),
  folder = "glimma-plots",
  html = "MDS-Plot",
  launch = TRUE,
  ...
)

Arguments

x	the DGEList containing the gene expressions.
top	the number of top most variable genes to use.
labels	the labels for each sample.
groups	the experimental group to which samples belong.
gene.selection	"pairwise" if most variable genes are to be chosen for each pair of samples or "common" to select the same genes for all comparisons.
prior.count	average count to be added to each observation to avoid taking log of zero. Used only if log=TRUE.
main	the title of the 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.

Value

Draws a two-panel interactive MDS plot in an html page. The left panel contains the plot between two MDS dimensions, with annotations displayed on hover. The right panel contains a bar plot of the eigenvalues of each dimension, clicking on any of the bars will plot the corresponding dimension against the next dimension.

Author(s)

Shian Su, Gordon Smyth

Shians/Glimma documentation built on April 1, 2020, 5:46 a.m.