plot.tfbs.venndiagram {cobindR} | R Documentation |
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.
## 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/)