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cobindR (version 1.10.0)

plot.tfbs.venndiagram: 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

"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

References

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

See Also

plot.tfbs.heatmap