Plot a genomic region given a matrix
Arguments
- mat
a matrix where rows are coordinates and columns are metacells
- mc_colors
a vector of colors for the metacells (optional)
- colors
color pallette for the ATAC signal
- color_breaks
a vector of breaks for the color palette
- intervals
the plotted intervals (optional)
- resolution
the resolution of the plotted intervals (optional)
- dca_mat
a matrix with the differential cluster accessibility (DCA) for the plotted regions (optional). Output of
mct_diff_access_on_hc
.- n_smooth
number of genomic bins to use for smoothing the signal. Signal is smoothed by a rolling sum for each metacell (optional). Default is 20.
- n_pixels
number of pixels in the plot. The DCA regions would be extended by
ceiling(2 * nrow(mat) / n_pixels)
(optional).- gene_annot
whether to add gene annotations; these annotations rely on the existence of an
annots/refGene.txt
file in the genome's misha directory, and on the existence of an intervals set called "intervs.global.tss" in the genome's misha directory. (optional)