Visualize 'C' contact map
This function implements the
plot method for objects
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.
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
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.
NULL; this function is called for the side-effect of
creating the plot.
object that inherits from class
List of GRanges objects of data to display as annotation track(s)
the minimum range of values used to define the color palette
the maximum range of values used to define the color palette
define the maxrange and minrange values using the percentile of the interaction matrix
logical; plot the zero values
logical; show the NA values in gray
logical; do you want to log the data before plotting the heatmap
color for (low,mid,high) positive contact counts. Must be a vectore of size 3. mid can be NA
color for (low,mid,high) negative contact counts. Must be a vectore of size 3. mid can be NA
color for NA values
logical; add a grid on the heatmap
character; add a title to the
logical; display the contact values on the matrix. Useful for small matrices
optional. object that inherits from class
logical; display the names of the intervals. Useful for small matrices
N. Servant, B. Lajoie
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
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))
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.