Description Usage Arguments Value Examples
View source: R/arseq.pca.plot.R
Plots any two specified principal components. By default it plots the first two principal components.
1 2 3 4 5 6 7 8 | arseq.pca.plot(
dds,
intgroup = "arseq.group",
ntop = 500,
pc.a = 1,
pc.b = 2,
returnData = FALSE
)
|
dds |
DESeq2 object |
intgroup |
interesting groups: a character vector of names in colData(x) to use for grouping. |
ntop |
number of top genes to use for principal components, selected by highest row variance |
pc.a |
numeric: Defines the first principal component. Default:1 |
pc.b |
numeric: Defines the second principal component.Default:2 |
returnData |
should the function only return the data.frame of 'pc.a' and 'pc.b' with intgroup covariates for custom plotting (default is FALSE) |
ggplot of the two selected principal components
1 2 3 4 | ## Not run:
pca.plot <- arseq.pca.plot (example_dds, intgroup="treatment")
## End(Not run)
|
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