General Arguments
object |
Object. |
i |
An integer or numeric scalar. |
value |
Value to assign. |
x |
Object. |
... |
Additional arguments. |
alpha |
Adjusted P value ("alpha") cutoff. |
colData |
|
color |
Desired ggplot color scale. Must supply discrete values. When
set to |
counts |
Object containing a normalized counts matrix. |
dir |
Local directory path. |
direction |
Plot " |
fill |
Desired ggplot fill scale. Must supply discrete values. When set
to |
flip |
Flip x and y axes. |
gene2symbol |
|
genes |
Character vector of genes to include. These must match the rownames of the object. It is best practice to use the stable gene identifiers from Ensembl (e.g. "ENSG00000000003") and not the gene symbols. |
headerLevel |
R Markdown header level. |
interestingGroups |
Character vector denoting groups of interest that
define the samples. If left unset, defaults to |
lfcThreshold |
Log fold change ratio (base 2) cutoff threshold. |
limit |
Threshold to denote on the plot, using a dashed line. |
minCounts |
Minimum number of counts per gene in the counts matrix. |
normalized |
Character indicating which normalization method to apply:
|
ntop |
Number of top genes to label. |
passLimit |
Threshold to plot pass color marker. |
pointColor |
Default point color for the plot. |
results |
|
return |
Object class to return. Uses |
samples |
Character vector of samples to include. |
sigPointColor |
|
subtitle |
Subtitle of plot. |
title |
Title of plot. |
warnLimit |
Threshold to plot warning color marker. |
withDimnames |
A |
No value.
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