mapC: Visualize 'C' ontact map

In bioinfo-pf-curie/HiTC: High Throughput Chromosome Conformation Capture analysis

Description

Visualize 'C' contact map

Details

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.

Value

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

Author(s)

N. Servant, B. Lajoie

See Also

HTCexp-class, HTClist-class

Examples

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))

bioinfo-pf-curie/HiTC documentation built on May 17, 2019, 6:39 p.m.