cobindR (version 1.10.0)

plot.tfbs.heatmap: function to do plot a heatmap of overlaps between all specified PWMs

Description

plot.tfbs.heatmap plots a heatmap of overlaps between all specified PWMs. For each overlap, the significance is determined based on the hypergeometric test. If a file path is specified in pdf.name, the diagram will be written into the specified file.

Usage

"plot.tfbs.heatmap"(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, for which the overlap will be visualized. If no list is given, all PWMs in runObj are used.

include.empty.seqs

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

Warning

• unknown identifier if the list of PWMs contains unknown PWM identifiers a warning is given and the method stops
• no hits if no hits are found in the object, the method gives a warning and stops

Details

In this plot for each pair of PWMs the overlap of sequences with hits of the given PWMs is calculated. The number of sequences in each overlap are color-coded in the heatmap. For each overlap the significance is calculated using the hypergeometric test. If the significance is below 0.05 (or below 0.01), the corresponding field is marked with one (or two) *.

See Also

plot.tfbs.venndiagram