Description Usage Arguments Value
View source: R/plotting_functions.R
Build a multi-track pileup plot
1 2 3 4 5 |
gr_list |
A list of GRanges objects |
ucsc_loc |
A target location, in UCSC format (e.g. "chr1:533,235-552,687) |
highlight_loc |
A location to use for highlights in UCSC format |
padding |
A 2-element numeric vector with upstream and downstream padding around the ucsc_loc to extend the plotting window. |
gr_groups |
A vector indicating which group each GRanges object in gr_list belongs to. If NULL, will group all samples into a single track. |
group_colors |
A named vector, one per group, with colors for each group. Names should match values in gr_groups. |
norm |
Normalization for each group. Currently support is per-million ("PM") and "max". |
max_val |
A maximum value to use for scaling the y-values in each track. |
window_size |
Window bin size to use for region down-sampling. If NULL, will not downsample. |
window_mode |
If using window_size, what value to use for each window. Options are "max","mean", and "median". |
target_color |
The color of the background rectangle to highlight the region in ucsc_loc. |
highlight_color |
The color the background rectangle to highlight the region in highlight_loc. |
A ggplot2 plot object
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.