viewGSEA: Plot a figure of GSEA results for one gene set

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 a figure of the positions of the gene sets in the ranked gene list and the location of the enrichment score.

Usage

## S4 method for signature 'GSCA'
viewGSEA(
  object,
  gscName,
  gsName,
  ES.range = NULL,
  rankMetric.range = NULL,
  main.title = NULL,
  pheno.title = c("Postive", "Negative"),
  ESline.col = "FireBrick",
  hits.col = "black",
  rankMetric.col = "CadetBlue"
)

Arguments

object	A GSCA object.
gscName	A single character value specifying the name of the gene set collection where the gene set is.
gsName	A single character value specifying the name of the gene set to be plotted.
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.
main.title	A single character value specifying the main title of the GSEA plot. Default is the name of the gene set.
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".

Details

We suggest to print the names of top significant gene sets using the function getTopGeneSets before plotting the GSEA results.

Value

In the end, this function would draw a GSEA figure for specified gene set.

Examples

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

## summarize gsca
summarize(d7_gsca)

## print top significant gene sets in GO_MF
topGS_GO_MF <- getTopGeneSets(d7_gsca, "GSEA.results", gscs = "GO_MF", allSig=TRUE)

## view GSEA results for one gene set
## Not run: 
viewGSEA(d7_gsca, "GO_MF", topGS_GO_MF[["GO_MF"]][1])

## view GSEA results for the same gene set by user defined enrichment score range,
## ranked gene list range and enrichment score profile line color.
viewGSEA(d7_gsca, "GO_MF", topGS_GO_MF[["GO_MF"]][1],
ES.range = c(-1, 0), rankMetric.range = c(-5, 2),
ESline.col = "green")

## End(Not run)

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