bb_plotHicTriangle.Rdplots HiC interaction matrix in triangular format
bb_plotHicTriangle( hic, chrom, params = NULL, chromstart = NULL, chromend = NULL, resolution = "auto", zrange = NULL, palette = colorRampPalette(c("white", "dark red")), assembly = "hg19", width = NULL, height = NULL, x = NULL, y = NULL, just = c("left", "top"), norm = "KR", default.units = "inches", draw = T, dataType = "observed" )
| hic | path to .hic file or 3 column dataframe of counts |
|---|---|
| chrom | chromosome of region to be plotted, based on build (i.e. for hg19 just a number, for hg38 string like "chr8") |
| params | an optional "bb_params" object space containing relevant function parameters |
| chromstart | chromosome start of region to be plotted |
| chromend | chromosome end of region to be plotted |
| resolution | the width in bp of each pixel; for hic files, "auto" will attempt to choose a resolution based on the size of the region; for dataframes, "auto" will attempt to detect the resolution the dataframe contains |
| zrange | the range of interaction scores to plot, where extreme values will be set to the max or min |
| palette | ColorRamp palette to use for representing interaction scores |
| assembly | desired genome assembly |
| width | A numeric or unit object specifying the bottom width of the triangle |
| height | A numeric or unit object specifying the height of the triangle |
| x | A numeric or unit object specifying x-location |
| y | A numeric or unit object specifying y-location |
| just | a string or numeric vector specifying the justification of the viewport relative to its (x, y) location |
| norm | if giving .hic file, hic data normalization; must be found in hic file |
| default.units | A string indicating the default units to use if x, y, width, or height are only given as numerics |
| draw | A logical value indicating whether graphics output should be produced |
| dataType | type of data to be returned; options are "observed" and "oe" |