plotTop10: A wrapper function to plot top10 test results.

In xyang2uchicago/seq2pathway: a novel tool for functional gene-set (or termed as pathway) analysis of next-generation sequencing data

Description

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

Usage

  plotTop10(res,fdr=0.05,or=2,myfileID=NULL)

Arguments

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.

Author(s)

Xinan Holly Yang, Zhezhen Wang

Examples

  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)

xyang2uchicago/seq2pathway documentation built on Dec. 23, 2021, 7:14 p.m.