plotTop10 {seq2pathway} | R Documentation |
Plot a vertical bar plot of odds ratios with red lines indicates -log10(fdr adjusted p-value) of the top10 results ordered by FDR. This plot is sorted by -log10(FDR) from large to small
plotTop10(res,fdr=0.05,or=2,myfileID=NULL)
res |
A result table of FisherTest_GO_BP_MF_CC function, FisherTest_MsigDB function, single element of result list of gene2pathway_test function or any table with colnames : 'FDR', 'Fisher_odds', 'Intersect_gene'/'GeneSet' |
fdr |
A non-negative FDR cuttoff for the table 'res'. Default is 0.05. |
or |
A non-negative odds ratio cuttoff for the table 'res'. Default is 2. |
myfileID |
main title of the plot. Default is NULL. |
Xinan Holly Yang, Zhezhen Wang
data(dat_chip) data(GO_BP_list,package="seq2pathway.data") data(Des_BP_list,package="seq2pathway.data") newOntology <- list(GO_BP_list[1:200], Des_BP_list[1:200]) FS_test<- FisherTest_GO_BP_MF_CC(gs=as.vector(rownames(dat_chip)), Ontology="newOntology", newOntology=newOntology) plotTop10(FS_test$newOntology, fdr=.3)