buildXYData {Glimma} | R Documentation |
XY Data Object Builder
Description
Common processing steps for both MA, XY and volcano plots.
Expects a dataframe, table
, which contains two columns labelled xlab
and ylab
as well as a unique identifier column labelled gene
.
Usage
buildXYData(
table,
status,
main,
display.columns,
anno,
counts,
xlab,
ylab,
status.cols,
sample.cols,
groups,
transform.counts
)
Arguments
table |
dataframe containing xlab and ylab columns for plotting.
|
status |
vector of length nrow(x) indicating the status of each gene.
By default genes in the summary plot are coloured based on its differential expression status
using an adjusted p-value cutoff of 5% by calling the limma::decideTests function, where
the value of -1 marks down-regulated genes, 0 marks genes with no expression difference, and
1 marks up-regulated genes.
|
main |
character string for the main title of summary plot.
|
display.columns |
character vector containing names of columns from anno from
which to display in mouseover tooltips and table.
|
anno |
dataframe with nrow(x) rows containing gene annotations.
|
counts |
numeric matrix with nrow(x) rows containing gene expression values.
This can be used to replace the gene counts from dge$counts , i.e. you may have
log-rpkm values stored in a different object that you wish to use.
|
xlab |
character string for the x-axis label of summary plot.
|
ylab |
character string for the y-axis label of summary plot.
|
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 .
|
groups |
vector of length ncol(dge) representing categorisation of samples in
expression plot.
|
transform.counts |
the type of transformation used on the counts - "logcpm" for using edgeR::cpm(counts, log=TRUE) ;
"cpm" for edgeR::cpm(counts) ; "rpkm" for edgeR::rpkm(counts) ; "logrpkm" for edgeR::rpkm(counts, log=TRUE) ; and "none" for no transformation). Defaults to "logcpm".
|
Value
object for XY plot internal use
[Package
Glimma version 2.4.0
Index]