reportAll: Write HTML reports for both enrichment and network analyses

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

Description

This function can create shiny reports for both gene sets enrichment analysis and network analysis.

Usage

reportAll(
  gsca = NULL,
  nwa = NULL,
  TSOrder = NULL,
  specificGeneset = NULL,
  cutoff = NULL,
  gseaPlot = FALSE,
  para = list(output = "pdf", ES.range = NULL, rankMetric.range = NULL, ESline.col =
    "FireBrick", hits.col = "black", rankMetric.col = "CadetBlue"),
  reportDir = "AnalysisReport"
)

Arguments

gsca	An analyzed GSCA object or a list of analyzed GSCA objects.
nwa	An NWA object or a list of NWA objects.
TSOrder	A character specifying the visulization order of 'Time Series' data in shiny report. Only works when reporting for 'Time Series' data, default is the ID order in 'expInfor'.
specificGeneset	A named list of specific gene sets. See viewEnrichMap,GSCA-method for details.
cutoff	A numeric value between 0 and 1. This parameter is setted as a cutoff of edge weight in the enrichment map for better visualization. When the edge weight, namely the Jaccard coefficient between two gene sets, is less than this cutoff, this edge would not be showed in the enrichment map.
gseaPlot	A logical value to choose whether make gsea plot for significant gene sets, default is FALSE.
para	A list of parameters for gsea plot. See plotGSEA for details.
reportDir	A single character value specifying the path to store reports. By default, the enrichment analysis reports will be stored in the directory called "GSCAReport". Once launching, the directory will be generated automatically containing an R code file named app.R, an RDdata object named results.RData storing all basic results which can be loaded into R with readRDS() function and a folder named gsea_plots containing gsea plots for all significant gene sets.

Value

In the end, this function would generate a html report.

Examples

## Not run: 
## load data
data(d7_gsca, d7_nwa, gscaTS, nwaTS)

## Example1: report both gsca and nwa
reportAll(gsca=d7_gsca, nwa=d7_nwa)

## Example2: report gscaTS
reportAll(gsca=gscaTS)

## Example3: report nwaTS
reportAll(nwa=nwaTS)

## Example4: report both gscaTS and nwaTS
reportAll(gsca=gscaTS, nwa=nwaTS)

## Example5: change order for time series data
reportAll(gsca=gscaTS, TSOrder=names(gscaTS)[c(3, 1, 2)])
reportAll(nwa=nwaTS, TSOrder=names(nwaTS)[c(3, 2, 1)])

## Example6: view specificGeneset enrichment map for gscaTS using reportAll
library(igraph)
## As told previously, specificGeneset needs to be a subset of all analyzed gene sets
## which can be roughly gotten by:
tmp <- getTopGeneSets(gscaTS[[1]], resultName = "GSEA.results",
                      gscs=c("GO_BP"), ntop = 20000, allSig = FALSE)
## In that case, we can define specificGeneset as below:
GO_BP_geneset <- tmp$GO_BP[c(4:10, 20:30)]
## the name of specificGenesets also needs to match with the names of tmp
specificGeneset <- list("GO_BP"=GO_BP_geneset)
reportAll(gsca=gscaTS, specificGeneset=specificGeneset)

## Example7: report gscaTS using a cutoff to filter away edges with small weight
reportAll(gsca=gscaTS, cutoff = 0.03)

## End(Not run)

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