plot.tfbs.venndiagram {cobindR}R Documentation

function visualize the overlaps of PWM hits over the sequences.

Description

The distribution of PWM hits over the sequences is visualized as Venn diagram. If a list of PWM names is provided, only these PWMs are included in the Venn diagram. If include.empty.seqs == TRUE, sequences without hits of the specified PWMs are also included in the diagram. If a file path is specified in pdf.name, the diagram will be written into the specified file.

Usage

## S4 method for signature 'cobindr'
plot.tfbs.venndiagram(x, pwms, include.empty.seqs = FALSE)

Arguments

x

an object of the class "cobindr", which will hold all necessary information about the sequences and the hits.

pwms

list of PWMs, which shall be visualized in the Venn-Diagram. If no list is given, all PWMs in the runObj are used. The package "VennDiagram" only allows Venn plots with up to 4 elements.

include.empty.seqs

logical flag, if include.empty.seqs == TRUE, sequences without hits of the specified PWMs are also included in the diagram.

Warning

Author(s)

Manuela Benary <manuela.benary@cms.hu-berlin.de

References

using the package "VennDiagram" (http://www.biomedcentral.com/1471-2105/12/35/)

See Also

plot.tfbs.heatmap


[Package cobindR version 1.20.0 Index]