plot.tfbs.venndiagram: function visualize the overlaps of PWM hits over the...
In cobindR: Finding Co-occuring motifs of transcription factor binding sites

Description Usage Arguments Warning Author(s) References See Also

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.

1 2	## S4 method for signature 'cobindr' plot.tfbs.venndiagram(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, 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.

unknown identifier: if the list of PWMs contains unknown PWM identifiers a warning is given and the method stops
too many PWMs: if more than 4 PWMs are listed 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

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

plot.tfbs.heatmap

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