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

- 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

### 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 1.18.0 Index]