% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/eigen_plot.R
\name{trans.compartment.plot}
\alias{trans.compartment.plot}
\title{trans.compartment.plot}
\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{
\item{exp}{A GENOVA experiment-object}

\item{chrom1, chrom2}{Which chromosome-combination should be drawn}

\item{arm1, arm2}{which chromosome arm: 'p' or 'q' (for acrocentric this should be set to 'q')}

\item{cut.off}{maximum value for the heatmap}

\item{invert}{whether the compartment score should be inverted, this should be a vector with a logical value for each chromosome}

\item{color.scheme}{color scheme that should be used, defaults to fall, other values result in white-red gradient}

\item{cs.lim}{y-axis limit for the compartment-score, if unset (NULL) will default to the maximum absolute value}

\item{chip}{A data.frame, containg ChIP-seq peaks of active histone marks to correctly orient A/B compartments}
}
\description{
Draw interchromosomal interaction heatmap for a chromosome (arm) with corresponding (cis) compartment scores
}
\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)
}
