Description Usage Arguments Value Author(s) See Also
View source: R/plot_gsea.leadingedge.HCL.auto.R
Automated method for doing a hierarchical clustering of genesets, based on each sets leading edge genes, for all gsea results in a list of gsea results, over a range of different best N, FDR, P, FWER thresholds, and for up/down genesets.
1 2 |
x |
either a gsea list, or a list of gsea lists. see import.gsea |
file |
either the path to a pdf file which will be created, or NULL to use the current plotting device |
N |
vectors of 0 or more thresholds to use. eg N=c(50, 100) means plot the top 50, or the |
FDR |
vectors of 0 or more thresholds to use. eg N=c(50, 100) means plot the top 50, or the |
P |
vectors of 0 or more thresholds to use. eg N=c(50, 100) means plot the top 50, or the |
FWER |
vectors of 0 or more thresholds to use. eg N=c(50, 100) means plot the top 50, or the top 100 genesets |
max.distance |
(experimental) threshold to filter out genesets that are poorly connected to each other. This is a distance threshold, so 1.0 means all genesets, 0.9 is a good place to start. |
makes a number of plots to a pdf file, or the current plotting device
Mark Cowley, 2009-09-03
plot_gsea.leadingedge.HCL
, gsea.leadingedge.distance
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