plot_contact_map: Plots simple contact map or fold-change contact map with log2...

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

Description

Plots simple contact map or fold-change contact map with log2 scale.

Usage

plot_contact_map(
  contact.map,
  fc = FALSE,
  breaks = 100,
  zeros.na = TRUE,
  colors.pal = c("white", "red"),
  useRaster = TRUE,
  ...
)

Arguments

contact.map	numeric matrix (with non-negative entries) to be plotted
fc	logical whether given matrix is fold change
breaks	numeric number of breaks on color scale
colors.pal	colors for pallette
useRaster	logical if TRUE (default) lower quality image is produced, but the process is much faster and resulting file uses little space
title	character plot title

See Also

image_plot_na for function handling heatmap plotting

Examples

# get sample contact map (MSC replicate 1) for chromosome 18
mtx1.sparse <- DIADEM::sample_hic_maps[["MSC-HindIII-1_40kb-raw"]][["18"]]
# convert to dense
mtx1 <- sparse2dense(mtx1.sparse[c("i","j","val")], N = 1952)
plot_contact_map(mtx1)
# now make fold-change matrix
# get another sample contact map (MSC replicate 2) for chromosome 18
mtx2.sparse <- DIADEM::sample_hic_maps[["MSC-HindIII-2_40kb-raw"]][["18"]]
merged <- base::merge(mtx1.sparse, mtx2.sparse, by = c("i", "j"))
merged$fc <- merged$val.x / merged$val.y
fc.mtx <- sparse2dense(merged[c("i","j","fc")], N = 1952)
plot_contact_map(fc.mtx, fc = TRUE, colors.pal = c("blue","white","red"))

rz6/CopulaHiC documentation built on Dec. 31, 2019, 9:19 a.m.