pcascree: Scree plot of the PCA on the samples
In pcaExplorer: Interactive Visualization of RNA-seq Data Using a Principal Components Approach
Description
Usage
Arguments
Value
Examples
Description
Produces a scree plot for investigating the proportion of explained variance, or
alternatively the cumulative value
Usage
1
Arguments
obj
A prcomp object
type
Display absolute proportions or cumulative proportion. Possible values:
"pev" or "cev"
pc_nr
How many principal components to display max
title
Title of the plot
Value
An object created by ggplot, which can be assigned and further customized.
Examples
1
2
3
4
5
dds <- makeExampleDESeqDataSet_multifac(betaSD_condition = 3, betaSD_tissue = 1)
rlt <- DESeq2::rlogTransformation(dds)
pcaobj <- prcomp(t(SummarizedExperiment::assay(rlt)))
pcascree(pcaobj, type = "pev")
pcascree(pcaobj, type = "cev", title = "Cumulative explained proportion of variance - Test dataset")
pcaExplorer documentation built on Nov. 8, 2020, 5:29 p.m.
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Description Usage Arguments Value Examples
Description
Produces a scree plot for investigating the proportion of explained variance, or alternatively the cumulative value
Usage
1 |
Arguments
obj |
A |
type |
Display absolute proportions or cumulative proportion. Possible values: "pev" or "cev" |
pc_nr |
How many principal components to display max |
title |
Title of the plot |
Value
An object created by ggplot, which can be assigned and further customized.
Examples
1 2 3 4 5 | dds <- makeExampleDESeqDataSet_multifac(betaSD_condition = 3, betaSD_tissue = 1)
rlt <- DESeq2::rlogTransformation(dds)
pcaobj <- prcomp(t(SummarizedExperiment::assay(rlt)))
pcascree(pcaobj, type = "pev")
pcascree(pcaobj, type = "cev", title = "Cumulative explained proportion of variance - Test dataset")
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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