Reference Code backup Executable files
This tools takes the default output of multiBamSummary or multiBigwigSummary, and computes the pairwise correlation among samples. Results can be visualized as scatterplots or as a heatmap of correlation coefficients
plotCorrelation [-h] --corData FILE --corMethod {spearman,pearson} --whatToPlot {heatmap,scatterplot} [--plotFile FILE] [--skipZeros] [--labels sample1 sample2 [sample1 sample2 ...]] [--plotTitle PLOTTITLE] [--plotFileFormat FILETYPE] [--removeOutliers] [--version] [--outFileCorMatrix FILE] [--plotHeight PLOTHEIGHT] [--plotWidth PLOTWIDTH] [--zMin ZMIN] [--zMax ZMAX] [--colorMap] [--plotNumbers] [--xRange XRANGE XRANGE] [--yRange YRANGE YRANGE] [--log1p]
plotCorrelation is a tool from the deepTools suite. The information on this page is based on deepTools version 3.5.1.
–corData, -in Compressed matrix of values generated by multiBigwigSummary or multiBamSummary
–plotFile, -o File to save the heatmap to. The file extension determines the format, so heatmap.pdf will save the heatmap in PDF format. The available formats are: .png, .eps, .pdf and .svg.
–corMethod, -c Possible choices: spearman, pearson
Correlation method.
–whatToPlot, -p Possible choices: heatmap, scatterplot
Choose between a heatmap or pairwise scatter plots
–skipZeros By setting this option, genomic regions that have zero or missing (nan) values in all samples are excluded.
–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.
–removeOutliers If set, bins with very large counts are removed. Bins with abnormally high reads counts artificially increase pearson correlation; that’s why, multiBamSummary tries to remove outliers using the median absolute deviation (MAD) method applying a threshold of 200 to only consider extremely large deviations from the median. The ENCODE blacklist page (https://sites.google.com/site/anshulkundaje/projects/blacklists) contains useful information about regions with unusually high countsthat may be worth removing.
–version show program’s version number and exit
–outFileCorMatrix Save matrix with pairwise correlation values to a tab-separated file.
–zMin, -min Minimum value for the heatmap intensities. If not specified, the value is set automatically
–zMax, -max Maximum value for the heatmap intensities.If not specified, the value is set automatically
–colorMap Color map to use for the heatmap. Available values can be seen here: http://matplotlib.org/examples/color/colormaps_reference.html
–plotNumbers If set, then the correlation number is plotted on top of the heatmap. This option is only valid when plotting a heatmap.