hicPlotTADs output is similar to a genome browser screen-shot that besides the usual genes, and score data (like bigwig or bedgraph files) also contains Hi-C data. The plot is composed of tracks that need to be specified in a configuration file. Once the tracks file is ready, hicPlotTADs can be used as follows:
$ hicPlotTADs --tracks tracks.ini --region chrX:99,974,316-101,359,967 \ -t 'Marks et. al. TADs on X' -o tads.pdf
The following is a template for the configuration file which is based on .ini configuration files. Each track is defined by a section header (for example [hic track]), followed by parameters specific to the section as color, title, etc.
# lines that start with '#' are comment lines # and are not interpreted by the program # the different tracks are represented by sections in this file # each section starts with a header of the form [hic] # the content of the section label (in the previous example 'hic') is irrelevant for # plotting and only used to tell the user when something goes wrong. # There are two exceptions for this, the [x-axis] and the [spacer] sections # that use the section label to determine the action. [hic] file = hic.h5 title = Hi-C colormap = RdYlBu_r depth = 100000 # optional arguments min_value =2.8 max_value = 3.0 # transform options are log1p, log and -log transform = log1p boundaries_file = conductance_vs_hic/boundaries_all.bed x labels = yes type = interaction # in case it can not be guessed by the file ending file_type = hic_matrix # show masked bins plots as white lines # those bins that were not used during the correction # the default is to extend neighboring bins to # obtain an aesthetically pleasant output show_masked_bins = yes # optional, if the values in the matrix need to be scaled the # following parameter can be used scale factor = 1 [x-axis] # optional fontsize=20 # optional, options are top or bottom where=top # to insert a space simple add a # section title [spacer] [spacer] #optional width = 0.1 # You can also show the interactions as arcs between start and end bins. # for this simply write the interactions in the Ginteraction format (HiCExport) # and add the file here [interactions] file = Ginteractions.tsv file_type = links width = 10 color = black title = HAS manual interactions line width = 1 [bigwig] file = file.bw title = RNA-seq color = black width = 1.5 # optional values min_value = 0 max_value = auto # for each bin the average value is taken. The number of # bins applies for the range being plotted. For example # if 1Mb is plotted, then the average is computed for regions # of 1000000/500 = 2000 bp number of bins = 500 nans to zeros = True # options are: line, points, fill. Default is fill # to add the preferred line width or point size use: # type = line:lw where lw (linewidth) is float # similary points:ms sets the point size (markersize (ms) to the given float type = line # type = line:0.5 # type = points:0.5 # Default is yes, set to 'no' to turn off the visualization of # text showing the data range (eg. 0 - 100) for the track show data range = yes # in case it can not be guessed by the file ending # the file_type needs to be added file_type = bigwig [simple bed] file = file.bed title = peaks color = read # optional boder color. Set to none for no border color border_color = black width = 0.5 # optional. If not given is guessed from the file ending file_type = bed [genes] # example of a genes track # has the same options as a simple # bed but if the type=genes is given # the the file is interpreted as gene # file. If the bed file contains the exon # structure then this is plotted. Otherwise # a region **with direction** is plotted. file = genes.bed title = genes color = darkblue width = 5 # optional # to turn off/on printing of labels labels = off # options are 'genes' or 'domains'. type = genes # If not given is guessed from the file ending file_type = bed # optional: font size can be given if default are not good fontsize = 10 [chrom states] # this is a case of a bed file that is plotted 'collapsed' # useful to plot chromatin states if the bed file contains # the color to plot file = chromatinStates.bed title = chromatin states # color is replaced by the color in the bed file # in this case color = black # optional boder color. Set to none for no border color border_color = black # default behaviour when plotting intervals from a # bed file is to 'expand' them such that they # do not overlap. The display = collapsed # directive overlaps the intervals. display = collapsed width = 0.3 [bedgraph] file = file.bg title = bedgraph track color = green width = 0.2 # optional. Default is yes, set to no to turn off the visualization of data range show data range = yes # optional, otherwise guessed from file ending file_type = bedgraph [bedgraph matrix] # a bedgraph matrix file is like a bedgraph, except that per bin there # are more than one value separated by tab: E.g. # chrX 18279 40131 0.399113 0.364118 0.320857 0.274307 # chrX 40132 54262 0.479340 0.425471 0.366541 0.324736 # bedgraph matrices are produced by hicFindTADs file = spectra_conductance.bm title = conductance spectra width = 1.5 orientation = inverted min_value = 0.10 max_value = 0.70 # if type is set as lines, then the TAD score lines are drawn instead # of the matrix # set to lines if a heatmap representing the matrix # is not wanted type = lines file_type = bedgraph_matrix [vlines] # vertical dotted lines from the top to the bottom of the figure # can be drawn. For this a bed file is required # but only the first two columns (chromosome name and start # are used. # vlines can also be given at the command line as a list # of genomic positions. However, sometimes to give a file # is more convenient in case many lines want to be plotted. file = regions.bed type = vlines