plot.tfbs.heatmap: function to do plot a heatmap of overlaps between all...
In cobindR: Finding Co-occuring motifs of transcription factor binding sites

Description Usage Arguments Details Warning Author(s) See Also

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.

1 2	## S4 method for signature 'cobindr' plot.tfbs.heatmap(x, pwms, include.empty.seqs = FALSE)

`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.

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) *.

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

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

plot.tfbs.venndiagram

cobindR documentation built on April 28, 2020, 6:40 p.m.