bb_plotManhattan.Rdplots a Manhattan plot
bb_plotManhattan( bed, pVals, params = NULL, chrom = NULL, chromstart = NULL, chromend = NULL, assembly = "hg19", fillcolor = "black", pch = 19, space = 0.01, cex = 0.25, ymax = 1, range = NULL, sigVal = 5e-08, sigLine = F, sigCol = NULL, x = NULL, y = NULL, width = NULL, height = NULL, just = c("left", "top"), default.units = "inches", draw = T, ... )
| bed | data for Manhattan plot, can be any data in BED format or a GRanges |
|---|---|
| pVals | name of column in bedfile of corresponding p-values (will be converted to -log(10) space) |
| params | an optional "bb_params" object space containing relevant function parameters |
| chrom | string of specific chromosome to zoom in on according to genome build (Ex: hg19 = "chr1"); if NULL all chromosomes found in data will be plotted |
| chromstart | if single chromosome specified, start of region to be plotted |
| chromend | if single chromosome specified, end of region to be plotted |
| assembly | default genome assembly as a string or a bb_assembly object |
| space | the space between each chromsome as a fraction of the width of the plot |
| cex | number indiciating the amount by which points should be scaled relative to the default |
| ymax | fraction of max y value to set as height of plot |
| range | y-range of p-values to plot (c(min, max)) |
| sigVal | numeric indicating the significance level |
| sigLine | logical indicating whether to draw a line at the significance level |
| sigCol | single color for coloring significant values |
| x | A numeric or unit object specifying x-location |
| y | A numeric or unit object specifying y-location |
| width | A numeric or unit object specifying width |
| height | A numeric or unit object specifying height |
| just | A string or numeric vector specifying the justification of the viewport relative to its (x, y) location: "left", "right", "centre", "center", "bottom", "top" |
| 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 |
| colors | single color, vector of colors, or color palette |
| transp | transparency of colors |