Description Usage Arguments Value Warning Author(s) See Also Examples
View source: R/post_analysis.R
Given a list of two to five GO terms, overlap_GO() will produce a Venn diagram showing the counts of overlapping genes associated with those GO terms.
1 | overlap_GO(go_ids, result, filename=NULL, mar=rep(0.1, 4), ...)
|
go_ids |
A character vector of GO term identifiers to compare. For instance,
|
result |
The output of |
filename |
The output filename where the Venn diagram will be saved. Default is NULL, displaying the Venn diagram on screen. |
mar |
The margins around the Venn diagram. Some Venn diagrams place the GO term labels outside the visible frame. |
... |
Further parameters forwarded to |
Returns the output of the venn.diagram()
function.
An error is returned if the list of GO term identifiers contains less than
2 elements or more than 5, as the underlying venn.diagram()
method
does not support values outside that range.
Kevin Rue-Albrecht
Method venn.diagram
.
1 2 3 4 5 6 7 8 9 10 11 12 | # load the sample output data with p.values computed
data(AlvMac_results.pVal)
# filter for Biological Processes associated with 5+ genes and <=0.05 P-value
filtered_results <- subset_scores(
result=AlvMac_results.pVal, total_count=5, p.val=0.05,
namespace="BP")
# Venn diagram of overlapping genes between top 5 GO terms
overlap_GO(
go_ids=head(filtered_results$GO$go_id, n=5),
result=filtered_results, filename="VennDiagram.tiff")
|
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