mapC: Visualize 'C' ontact map
In HiTC: High Throughput Chromosome Conformation Capture analysis

Description Details Value For HTCexp and HTClist objects For HTCexp objects only For HTClist objects only Author(s) See Also Examples

Visualize 'C' contact map

This function implements the plot method for objects of class HTCexp and HTClist.

By default, the trim.range value is fixed so that the 98th percentile (resp. 2th percentile) of each interaction matrix is discarded. It therefore allow to remove the extreme values from the matrix, but each map is plotted independently. If the maxrange argument is set, data higher that this threshold will be fixed to the maxrange value for all maps. In addition, color ranges are ajusted in a way that all maps are plotted within the same color range allowing visual maps comparison.

The HTCexp and HTClist are not represented in the same way. The heatmap view is used to display the HTClist objects in two dimension. This view is mainly useful to have an overview of the data, as Hi-C data. The triangle view is used for HTCexp only and represent the top-right part the interaction matrix. If two HTCexp objects are specified, they will be displayed in order to compare both contact maps. The two maps have to be binned to ensure comparison between genomic ranges.

Annotation tracks can be added to both views. In case of binned data, the exact genomic positions of each features are takken into account. Otherwise, the 'C' intervals which overlap with the annotation features are colored.

Returns NULL; this function is called for the side-effect of creating the plot.

For `HTCexp` and `HTClist` objects

x: object that inherits from class HTCexp or HTClist
tracks: List of GRanges objects of data to display as annotation track(s)
minrange: the minimum range of values used to define the color palette
maxrange: the maximum range of values used to define the color palette
trim.range: define the maxrange and minrange values using the percentile of the interaction matrix
show.zero: logical; plot the zero values
show.na: logical; show the NA values in gray
log.data: logical; do you want to log the data before plotting the heatmap
col.pos: color for (low,mid,high) positive contact counts. Must be a vectore of size 3. mid can be NA
col.neg: color for (low,mid,high) negative contact counts. Must be a vectore of size 3. mid can be NA
col.na: color for NA values
grid: logical; add a grid on the heatmap
title: character; add a title to the HTCexp plot(s)
value: logical; display the contact values on the matrix. Useful for small matrices

For `HTCexp` objects only

y: optional. object that inherits from class HTCexp.

For `HTClist` objects only

names: logical; display the names of the intervals. Useful for small matrices

N. Servant, B. Lajoie

HTCexp-class, HTClist-class

data(Nora_5C)

## Contact map
## HTClist view
mapC(E14)

## HTCexp view
mapC(E14$chrXchrX)

## Play with contrast and color
mapC(E14$chrXchrX, maxrange=100, col.pos=c("black","red","yellow"))

## Add annotation and change view
require(rtracklayer)
exDir <- system.file("extdata", package="HiTC")
gene <- import(file.path(exDir,"refseq_mm9_chrX_98831149_103425150.bed"), format="bed")
mapC(E14$chrXchrX, tracks=list(Refseq=gene))

## Compare two samples
mapC(binningC(E14$chrXchrX), binningC(MEF$chrXchrX), tracks=list(Refseq=gene))