plot_regions: Plots regions (TADs or Long Range interactions) on contact...

In rz6/DIADEM: Hi-C differential analysis via dependency modelling of chromatin interactions with generalized linear models

Description

Plots regions (TADs or Long Range interactions) on contact map.

Usage

plot_regions(regions, pal.colors = NULL, lty = 1, lwd = 0.5)

Arguments

regions

data frame or matrix with 2 (+1) or 4 (+1) columns; 2 columns format is for tads - first column is start bin, second column is end bin; 4 columns format is for LR interactions (rectangle like regions) - columns 1,2 are start and end bin of first interacting region, columns 3,4 are start and end bin of second interacting region; Last column (optional) is category column - like effect column with depletion, no.change, enrichment values to color TADs or LR interactions accordingly

pal.colors

character vector of colors if additional category column is specified - how to color categories

See Also

plot_contact_map, plot_diff_map for plotting contact maps or differential_interactions for determining and plotting p-value map with differential interactions

Examples

# plot contact map or differential map - see ?plot_diff_map
plot_diff_map(dense, sqrt.transform = TRUE)
# then get tads and plot them
tads <- DIADEM::sample_tads[["MSC-HindIII-1_40kb-raw"]]
tads18 <- tads[tads$name == "18",]
plot_regions(tads18[c("start","end")])
# for plotting differential interactions see ?differential_interactions

rz6/DIADEM documentation built on Dec. 31, 2019, 3:51 a.m.