plot_pathway {RVA}

Pathway analysis and visualization

Description

This is the function to do pathway enrichment analysis (and visualization) with rWikipathways (also KEGG, REACTOME & Hallmark) from a summary statistics table generated by differential expression analysis like limma or DESeq2.

Usage

plot_pathway(
  data = ~df,
  comp.names = NULL,
  gene.id.type = "ENSEMBL",
  FC.cutoff = 1.2,
  FDR.cutoff = 0.05,
  FCflag = "logFC",
  FDRflag = "adj.P.Val",
  Fisher.cutoff = 0.1,
  Fisher.up.cutoff = 0.1,
  Fisher.down.cutoff = 0.1,
  plot.save.to = NULL,
  pathway.db = "rWikiPathways",
  customized.pathways = NULL,
  ...
)

Arguments

data

A summary statistics table (data.frame) or data.list generated by DE analysis software like limma or DEseq2, where rownames are gene id.

comp.names

A character vector containing the comparison names corresponding to the same order of the data.list. Default = NULL.

gene.id.type

The gene id format in data should be one of: ACCNUM, ALIAS, ENSEMBL, ENSEMBLPROT, ENSEMBLTRANS, ENTREZID, ENZYME, EVIDENCE, EVIDENCEALL, GENENAME, GO, GOALL, IPI, MAP, OMIM, ONTOLOGY, ONTOLOGYALL, PATH, PFAM, PMID, PROSITE, REFSEQ, SYMBOL, UCSCKG, UNIGENE, UNIPROT.

FC.cutoff

The fold change cutoff (numeric) selected to subset summary statistics table. Default = 1.5.

FDR.cutoff

The FDR cutoff selected (numeric) to subset summary statistics table. Default = 0.05.

FCflag

The column name (character) of fold change information, assuming the FC is log2 transformed. Default = "logFC".

FDRflag

The column name (character) of adjusted p value or FDR. Default = "adj.P.Val".

Fisher.cutoff

The FDR cutoff selected (numeric) for the pathway enrichment analysis' Fisher's exact test with all determined Differentially Expressed (DE) genes by FC.cutoff and FDR.cutoff.

Fisher.up.cutoff

The FDR cutoff selected (numeric) for the pathway enrichment analysis' Fisher's exact test with the upregulated gene set.

Fisher.down.cutoff

The FDR cutoff selected (numeric) for the pathway enrichment analysis' Fisher's exact test with the downregulated gene set.

plot.save.to

The address to save the plot from simplified cutoff combination with FDR of 0.01, 0.05, 0.1, and 0.2.

pathway.db

The databse to be used for encrichment analysis. Can be one of the following, "rWikiPathways", "KEGG", "REACTOME", "Hallmark","rWikiPathways_aug_2020".

customized.pathways

the customized pathways in the format of two column dataframe (column name as "gs_name" and "entrez_gene") to be used in analysis.

...

pass on variables

Details

The function takes the summary statistics table and use user selected parameter based on check.cutoff to do pathway enrichment analysis

Value

The function returns a list of 5 objects:

1

result table from directional pathway enrichment analysis

2

result table from non-directional pathway enrichment analysis

3

plot from directional pathway enrichment analysis

4

plot from non-directional pathway enrichment analysis

5

plot combining both directional and non-directional plot

References

Xingpeng Li & Siddhartha Pachhai RVA - RNAseq Visualization Automation tool.

Examples

result <- plot_pathway(data = Sample_summary_statistics_table,
gene.id.type = "ENSEMBL",
FC.cutoff = 1.5,
p.cutoff = 0.05,
pathway.db = "rWikiPathways_aug_2020"
)