glimmaMA.DESeqDataSet: Glimma MA Plot

In Glimma: Interactive HTML graphics

Description

Draws a two-panel interactive MA plot from an DESeqDataSet object. This is a special case of the glimmaXY plot.

Usage

## S3 method for class 'DESeqDataSet'
glimmaMA(
  x,
  counts = DESeq2::counts(x),
  groups = extractGroups(colData(x)),
  status = NULL,
  anno = NULL,
  display.columns = NULL,
  status.cols = c("dodgerblue", "silver", "firebrick"),
  sample.cols = NULL,
  transform.counts = c("logcpm", "cpm", "rpkm", "none"),
  main = "MA Plot",
  xlab = "logCPM",
  ylab = "logFC",
  html = NULL,
  width = 920,
  height = 920,
  ...
)

Arguments

x	DESeqDataSet object from which summary statistics are extracted from to create summary (left) plot.
counts	numeric matrix with nrow(x) rows containing gene expression values.
groups	vector/factor representing the experimental group for each sample; see extractGroups for default value.
status	vector of length nrow(x) indicating the status of each gene.
anno	dataframe with nrow(x) rows containing gene annotations.
display.columns	character vector containing names of columns from anno from which to display in mouseover tooltips and table.
status.cols	vector of length 3 containing valid CSS strings for colours associated with status in the order of -1, 0 and 1.
sample.cols	character vector of length ncol(counts) containing valid CSS strings for colours associated with each sample to be displayed on the expression plot. If left unspecified, samples will be coloured according to groups.
transform.counts	the type of transform used on the counts log-cpm by default. edgeR::cpm(counts, log=TRUE); defaults to FALSE.
main	character string for the main title of summary plot.
xlab	character string for the x-axis label of summary plot.
ylab	character string for the y-axis label of summary plot.
html	character string for naming HTML file for exportation of widget. The extension should be included in the file name e.g. "file.html".
width	numeric value indicating width of widget in pixels.
height	numeric value indicating width of height in pixels.
...	addition unused arguments.

Details

The summary plot on the left represents gene-wise log-fold-change (logFC) on the y-axis versus average gene expression calculated as log-counts-per-million (logCPM) values. We call our summary plot an MA plot because this type of plot was originally referred to as an MA plot in the limma package, with the M-value representing logFC and A-value representing average expression - it has since been renamed to MD plot in the limma package. The expression plot on the right displays sample expression values for a single gene. Interactions with the htmlwidget include clicking on genes (points) in the summary plot to bring up associated sample expression values in the expression plot, as well as the summary statistics in the table below. Alternatively, users can interact with the table by clicking on genes (rows) to highlight genes in the summary plot, as well as bring up associated sample expression values in the expression plot. Briefly, other interactive features include a search box for the table, buttons to save plots and data (summary statistics and expression values), additional pop-up information when hovering on points in plots, and rescaling of the y-axis in the expression plot.

Value

htmlwidget object or NULL if html argument is specified.

See Also

glimmaMA, glimmaMA.MArrayLM, glimmaMA.DGEExact, glimmaMA.DGELRT

Examples

dge <- readRDS(
  system.file("RNAseq123/dge.rds", package = "Glimma"))

dds <- DESeq2::DESeqDataSetFromMatrix(
  countData = dge$counts,
  colData = dge$samples,
  rowData = dge$genes,
  design = ~group
)

dds <- DESeq2::DESeq(dds, quiet=TRUE)
glimmaMA(dds)

Glimma documentation built on Nov. 8, 2020, 6:13 p.m.