mapC {HiTC} | R Documentation

## Visualize 'C' ontact map

### 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))

[Package HiTC version 1.38.0 Index]