Description Usage Arguments Details Value
This is a collection of functions from the package "pcaGoPromoter". It calculates the principle components and plots them. It also calculates TF and GO term enrichments.
1 2 3 | pca_plot_enrich(expmatrix, groups, PCs = c(1, 2), main = "PCA plot",
percentage = 2.5, inputType = "geneSymbol", org = "Hs",
projectfolder = getwd())
|
expmatrix |
An input matrix with gene names as row names and sample names as column names. |
groups |
Define sample groups. |
PCs |
Principle components to plot (pick two). Defaults to PCs 1 and 2. |
main |
Main title of PCA plot. Defaults to "PCA plot". |
percentage |
Percentage of genes with top loadings to use for TF and GO enrichment analysis. Defauls to 2.5. |
inputType |
a character vector description the input type. Must be Affymetrix chip type, "geneSymbol" or "entrezID". The following Affymetrix chip type are supported: hgu133plus2, mouse4302, rat2302, hugene10st and mogene10st. Default is Affymetrix chip type "hgu133plus2". |
org |
a character vector with the organism. Can be "Hs", "Mm" or "Rn". Only needed if inputType is "geneSymbol" or "entrezID". See details. Default is "Hs". |
projectfolder |
File path where to save the tables to. Defaults to working directory. Here, it saves the output to a subfolder called "pcaGoPromoter". |
Both, PC plot (as .pdf) and tables (as tab delimited .txt) of enriched TFs and GO terms are saved by default to the working directory or to the given path.
A PCA plot and tables of enriched TFs and GO terms.
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