Reference Code backup Executable files
This tool takes the default output file of multiBamSummary or multiBigwigSummary to perform a principal component analysis (PCA).
plotPCA [-h] --corData FILE [--plotFile FILE] [--labels sample1 sample2 [sample1 sample2 ...]] [--plotTitle PLOTTITLE] [--plotFileFormat FILETYPE] [--plotHeight PLOTHEIGHT] [--plotWidth PLOTWIDTH] [--outFileNameData file.tab] [--ntop NTOP] [--PCs PCS PCS] [--log2] [--colors COLORS [COLORS ...]] [--markers MARKERS [MARKERS ...]] [--version] [--transpose | --rowCenter]
plotPCA is a tool from the deepTools suite. The information on this page is based on deepTools version 3.5.1.
–corData, -in Coverage file (generated by multiBamSummary or multiBigwigSummary)
–plotFile, -o File name to save the plot to. The extension determines the file format. For example: pca.pdf will save the PCA plot in PDF format. The available options are: .png, .eps, .pdf and .svg.
–labels, -l User defined labels instead of default labels from file names. Multiple labels have to be separated by spaces, e.g. –labels sample1 sample2 sample3
–plotTitle, -T Title of the plot, to be printed on top of the generated image. Leave blank for no title.
–plotFileFormat Possible choices: png, pdf, svg, eps
Image format type. If given, this option overrides the image format based on the plotFile ending. The available options are: png, eps, pdf and svg.
–outFileNameData File name to save the data underlying data for the average profile, e.g., myProfile.tab.
–rowCenter When specified, each row (bin, gene, etc.) in the matrix is centered at 0 before the PCA is computed. This is useful only if you have a strong bin/gene/etc. correlation and the resulting principal component has samples stacked vertically.
–version show program’s version number and exit