plotGSEA: Plot and save figures of GSEA results for top significant...

In CityUHK-CompBio/HTSanalyzeR2: HTSanalyzeR2: An R package for functional annotation, network analysis and time series analysis of high-throughput data

Description

This is a generic function.When implemented as the S4 method for objects of class GSCA, this function plots figures of the positions of genes of the gene set in the ranked gene list and the location of the enrichment score for top significant gene sets.

Usage

## S4 method for signature 'GSCA'
plotGSEA(
  object,
  gscs,
  ntop = NULL,
  allSig = FALSE,
  filepath = ".",
  output = "pdf",
  ES.range = NULL,
  rankMetric.range = NULL,
  pheno.title = c("Postive", "Negative"),
  ESline.col = "FireBrick",
  hits.col = "black",
  rankMetric.col = "CadetBlue",
  ...
)

Arguments

object	A GSCA object.
gscs	A character vector specifying the names of gene set collections whose top significant gene sets will be plotted.
ntop	A single integer or numeric value specifying how many gene sets of top significance will be plotted.
allSig	A single logical value. If 'TRUE', all significant gene sets (GSEA adjusted p-value < 'pValueCutoff' of slot 'para') will be plotted; otherwise, only top 'ntop' gene sets will be plotted.
filepath	A single character value specifying where to store GSEA figures.
output	A single character value specifying the format of output image: "pdf" or "png".
ES.range	A numeric vector for user-defined range of enrichment score showing in the top part of GSEA plot. Default is the range of actual enrichment score of result. However, users are also allowed to set by themselves for better comparison with other GSEA plots.
rankMetric.range	A numeric vector for user-defined range of ranked gene lists showing in the bottom part of GSEA plot. Default is the range of actual ranked gene lists of result. However, users are also allowed to set by themselves for better comparison with other GSEA plots.
pheno.title	A charater vector for user-defined phenotype names. Default is c("Positive", "Negative").
ESline.col	The color to be used for enrichment score profile line. Defaults to "FireBrick".
hits.col	The color to be used for hits line to show the position of hits. Defaults to "CadetBlue".
rankMetric.col	The color to be used for ranked metric line. Defaults to "CadetBlue".
...	Other arguments used by the function png or pdf such as 'width' and 'height'

Value

In the end, this function would plot GSEA figure and store them into the specified path.

Examples

## load a GSCA object(see the examples of analyze GSCA for details)
data(d7_gsca)

## summarize d7_gsca
summarize(d7_gsca)

## plot  significant gene sets in GO_MF and PW_KEGG
## Not run: 
plotGSEA(d7_gsca, gscs=c("GO_MF","PW_KEGG"), ntop=3, filepath=".")

## End(Not run)

CityUHK-CompBio/HTSanalyzeR2 documentation built on Dec. 3, 2020, 2:35 a.m.