trans.compartment.plot: trans.compartment.plot

In robinweide/GENOVA: GENOVA: expore the Hi-C

trans.compartment.plot

Description

Draw interchromosomal interaction heatmap for a chromosome (arm) with corresponding (cis) compartment scores

Usage

trans.compartment.plot(
  exp,
  chrom1,
  arm1 = "p",
  chrom2,
  arm2 = "p",
  cut.off = NULL,
  invert = c(F, F),
  color.scheme = "fall",
  cs.lim = NULL,
  chip = NULL
)

Arguments

exp	A GENOVA experiment-object
chrom1, chrom2	Which chromosome-combination should be drawn
arm1, arm2	which chromosome arm: 'p' or 'q' (for acrocentric this should be set to 'q')
cut.off	maximum value for the heatmap
invert	whether the compartment score should be inverted, this should be a vector with a logical value for each chromosome
color.scheme	color scheme that should be used, defaults to fall, other values result in white-red gradient
cs.lim	y-axis limit for the compartment-score, if unset (NULL) will default to the maximum absolute value
chip	A data.frame, containg ChIP-seq peaks of active histone marks to correctly orient A/B compartments

Note

# Plot a trans-compartment plot of the q-arms of chromosome 9 and 22 trans.compartment.plot(exp = Hap1_WT_40kb, chrom1 = 'chr9', arm1 = 'q', chrom2 = 'chr22', arm2 = 'q', cut.off = 10,chip = H3K27ac_peaks)

robinweide/GENOVA documentation built on March 14, 2024, 11:16 p.m.