Description Usage Arguments Value Examples
View source: R/plot_ES_score.R
It's very complicate,please don't use this unless you have a clear understanding of the mechanism for the GSEA especially for the ES core ,the running ES core, the gene sets ! you need to prepare many data by yourself, I really can't help you with them. #'
1 2 3 | plot_ES_score(imageType = "png", width = 680, height = 680, res = 200,
Ng = 12, N = 34688, phen1 = "control", phen2 = "case", Obs.RES,
Obs.indicator, obs.s2n, size.G, gs.names, Obs.ES, Obs.arg.ES, Obs.ES.index)
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imageType |
choose png,pdf,emf,tiff,jpeg,bmp |
Ng |
The number of the gene sets, (eg: 200~300 kegg pathway) |
N |
The number of the genes (probably 20,000~30,000 genes) |
phen1 |
The name for the first phenotype (default:control) |
phen2 |
The name for the second phenotype (default:case) |
Obs.RES |
A matrix, running ES score for each gene in specific gene Set. |
Obs.indicator |
A matrix, 0/1 shows whether a gene belong to a gene Set. |
obs.s2n |
A vector of sigal to noise value for each gene (sorted, and Z-score) |
size.G |
A vector for the size of each geneSet |
gs.names |
A vector for the name of each geneSet |
Obs.ES |
A vector for the maximal ES score of each gene Set. |
Obs.arg.ES |
A vector for the order of the gene shows maximal ES score of each gene Set. |
write some files
1 | #' plot_ES_score(imageType='png',width = 680,height = 680 ,Ng=12,N=34688,phen1='Control',phen2='case',Obs.RES,Obs.indicator,obs.s2n,size.G,gs.names,Obs.ES,Obs.arg.ES,Obs.ES.index)
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