Description Usage Arguments Author(s) Examples
Simple barplot that displays the enrichment of primary gene sets from a clusteredEnrichment result.
1 2 3 4 |
ceresult |
$results data frame returned by the clusteredEnrichmentGO() function. |
alpha |
Significance cutoff for primary gene set adjusted p-values, defaults to 0.05. |
t.alpha |
If a directionality bias has been determined via t-test on the log-fold-change of the gene set, which significance cutoff should be used for the display of that bias? (i.e. bar color) |
max_bars |
If set, scales the bar plot to provide space for max_bars... bars. Use to ensure uniform scaling when plotting multiple results with varying numbers of significant hits. |
top_n |
Plot only the most significant top_n results. Default is to show all results. |
only_positive_enrichment |
Defaults to TRUE: show only positive log-enrichments (i.e. no depleted terms). |
order_by_enrichment |
Defaults to TRUE: order significant hits by effect magnitude (enrichment) rather than significance. |
legend.title |
Title of the legend (only relevant if directionality bias of GO terms is included in the results). |
xlim |
Axis limit of the enrichment plot. Use to ensure uniform axis across multiple plots. |
lab_max_chars |
Maximum length of gene set names; longer names are truncated. |
Robert Sehlke
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | ## Not run:
# example for annotation matrix creation
# may be used interchangably with createGoMatrix()
gomatrix = createAnnotationMatrix( list("GO:0000042"=paste0("gene",1:6),
"GO:0000002"=paste0("gene",2:7),
"GO:0000009"=paste0("gene",6:12)) )
# example call for main function
res = clusteredEnrichmentGO(gomatrix,
geneset = paste0("gene",2:6),
universe = paste0("gene",1:12))
# example plot
plotClusteredEnrichment(res$results)
## End(Not run)
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