diff --git a/README.md b/README.md index 8895605..6677aea 100644 --- a/README.md +++ b/README.md @@ -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