plotTop10: A wrapper function to plot top10 test results.

Description Usage Arguments Author(s) Examples

View source: R/seq2pathway-internal.r

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

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  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

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  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)

xyang2uchicago/seq2pathway19 documentation built on April 18, 2019, 9:42 a.m.