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@akdemirlab
akdemirlab committed Oct 12, 2015
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Expand Up @@ -27,49 +27,49 @@ _HiCPlotter is purposefully designed with the least amount of dependencies to ma

Required parameters:

files: a list of filenames to be plotted.
name: a list of labels for the experiment.
chr: chromosome to be plotted.
output: prefix for the output file.
files (-f) : a list of filenames to be plotted.
name (-n) : a list of labels for the experiment.
chr (-chr) : chromosome to be plotted.
output (-o) : prefix for the output file.

Optional parameters:

verbose: print version and arguments into a file
histograms: a list of filenames to be plotted as histogram.
histLabels: a list of labels for the histograms.
fillHist: a list whether each histogram will be filled (1) or not (0:default).
histMax : a list of integer for maximum values of histograms.
start: retain after x-th bin (0:default).
end: continues until x-th bin (default: length of the matrix).
resolution: resolution of the bins (default: 100000).
tilePlots: a list of filenames to be plotted as tile plots.
tileLabels: a list of labels for the tile plots.
tileColors: a list of hexadecimal numbers for coloring the tile plots.
tileText: an integer whether text will be displayed above tiles (0:default) or not (1).
arcPlots: a list of filenames to be plotted as arc plots.
arcLabels: a list of labels for the arc plots.
arcColors: a list of hexadecimal numbers for coloring the arc plots.
highlights: an integer for enabling highlights on the plot (0:default), enable(1).
highFile: a file name for a bed file to highlight selected intervals.
peakFiles : a list of filenames to be plotted on the matrix.
window: an integer of distance to calculate insulation score.
tadRange: an integer of window to calculate local minima for TAD calls.
fileHeader: an integer for how many lines should be ignored in the matrix file (1:default).
fileFooter: an integer for how many lines should be skipped at the end of the matrix file (0:default).
smoothNoise: a floating-point number to clean noise in the data.
heatmapColor: an integer for choosing heatmap color codes: Greys(0), Reds(1), YellowToBlue(2), YellowToRed(3-default), Hot(4), BlueToRed(5).
cleanNANs: an integer for replacing NaNs in the matrix with zeros (1:default) or not (0).
plotTriangular: an integer for plotting rotated half matrix (1:default) or not (0).
plotTadDomains: an integer for plotting TADs identified by HiCPlotter (1) or not (0:default).
plotPublishedTadDomins: an integer for plotting TADs from Dixon et, al. 2012 (1:default) or not (0).
plotDomainsAsBars: an integer for plotting TADs as bars (1) instead of triangles (0:default)
highResolution: an integer whether plotting high resolution (1:default) or not (0).
plotInsulation: an integer for plotting insulation scores (0:default) or plot (1).
randomBins: an integer for plotting random resolution data (1:default) or not (0).
wholeGenome: an integer for plotting whole genome interactions (1:default) or not (0).
plotCustomDomains: a list of file names to be plotted beneath the matrix.
publishedTadDomainOrganism : an integer for plotting human (1:default) or mouse (0) TADs from Dixon et, al. 2012.
customDomainsFile: a list of filenames to be plotted as TADs for each experiments.
verbose (-v) : print version and arguments into a file
histograms (-hist) : a list of filenames to be plotted as histogram.
histLabels (-h) : a list of labels for the histograms.
fillHist (-fhist) : a list whether each histogram will be filled (1) or not (0:default).
histMax (-hm) : a list of integer for maximum values of histograms.
start (-s) : retain after x-th bin (0:default).
end (-e) : continues until x-th bin (default: length of the matrix).
resolution (-r) : resolution of the bins (default: 100000).
tilePlots (-t) : a list of filenames to be plotted as tile plots.
tileLabels (-tl) : a list of labels for the tile plots.
tileColors (-tc) : a list of hexadecimal numbers for coloring the tile plots.
tileText (-tt) : an integer whether text will be displayed above tiles (0:default) or not (1).
arcPlots (-a) : a list of filenames to be plotted as arc plots.
arcLabels (-al) : a list of labels for the arc plots.
arcColors (-ac) : a list of hexadecimal numbers for coloring the arc plots.
highlights (-high) : an integer for enabling highlights on the plot (0:default), enable(1).
highFile (-hf) : a file name for a bed file to highlight selected intervals.
peakFiles (-peak) : a list of filenames to be plotted on the matrix.
window (-w) : an integer of distance to calculate insulation score.
tadRange (-tr) : an integer of window to calculate local minima for TAD calls.
fileHeader (-fh) : an integer for how many lines should be ignored in the matrix file (1:default).
fileFooter (-ff) : an integer for how many lines should be skipped at the end of the matrix file (0:default).
smoothNoise (-sn) : a floating-point number to clean noise in the data.
heatmapColor (-hmc) : an integer for choosing heatmap color codes: Greys(0), Reds(1), YellowToBlue(2), YellowToRed(3-default), Hot(4), BlueToRed(5).
cleanNANs (-cn) : an integer for replacing NaNs in the matrix with zeros (1:default) or not (0).
plotTriangular (-ptr) : an integer for plotting rotated half matrix (1:default) or not (0).
plotTadDomains (-ptd) : an integer for plotting TADs identified by HiCPlotter (1) or not (0:default).
plotPublishedTadDomins (-pptd) : an integer for plotting TADs from Dixon et, al. 2012 (1:default) or not (0).
plotDomainsAsBars (-ptdb) : an integer for plotting TADs as bars (1) instead of triangles (0:default)
highResolution (-hR) : an integer whether plotting high resolution (1:default) or not (0).
plotInsulation (-pi) : an integer for plotting insulation scores (0:default) or plot (1).
randomBins (-rb) : an integer for plotting random resolution data (1:default) or not (0).
wholeGenome (-wg) : an integer for plotting whole genome interactions (1:default) or not (0).
plotCustomDomains (-pcd) : a list of file names to be plotted beneath the matrix.
publishedTadDomainOrganism (-ptdo) : an integer for plotting human (1:default) or mouse (0) TADs from Dixon et, al. 2012.
customDomainsFile (-pcdf) : a list of filenames to be plotted as TADs for each experiments.

# Input Files

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