report: Write HTML reports for enrichment or 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 is a generic function.

Usage

## S4 method for signature 'GSCA'
report(
  object,
  specificGeneset = NULL,
  cutoff = NULL,
  reportDir = "GSCAReport",
  gseaPlot = FALSE,
  para = list(output = "pdf", ES.range = NULL, rankMetric.range = NULL, ESline.col =
    "FireBrick", hits.col = "black", rankMetric.col = "CadetBlue")
)

## S4 method for signature 'NWA'
report(object, reportDir = "NWAReport")

Arguments

object	A 'GSCA' or 'NWA'object.
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.
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.
gseaPlot	A logical value to choose whether make gsea plot for significant gene sets or not, default is FALSE.
para	A list of parameters for gsea plot. See plotGSEA for details.

Details

When implemented as the method of class GSCA or NWA, this function produces reports for either the Gene Set Collection Analysis or the NetWork Analysis.

This will generate a shiny report including all the GSCA or NWA results.

For GSCA object, users can download the table of GSOA and/or GSEA result in different format such as 'csv' and 'pdf'. In GSEA result of this report, 'Pvalue' or 'Adjusted.Pvalue' equalling to 0 would be replaced by less than 1 divided by permutation times. The enrichment map could be modified according to the user's preferences such as layout, node, label, and etc. Details please see the vignette of our package.

For NWA object, the identified subnetwork could be modified according to the user's preferences in many ways such as layout, color, and etc. Details please see the vignette of our package.

Value

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

Examples

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

## Example1: report d7_gsca
## Not run: 
report(d7_gsca)

## End(Not run)

## Example2: report d7_gsca containing enrichment map with specificGeneset
tmp <- getTopGeneSets(d7_gsca, resultName = "GSEA.results", gscs=c("GO_MF"),
                      ntop = 20000, allSig = FALSE)
## In that case, we can define specificGeneset as below:
GO_MF_geneset <- tmp$GO_MF[20:35]
## the name of specificGenesets also needs to match with the names of tmp
specificGeneset <- list("GO_MF"=GO_MF_geneset)
## Not run: 
report(d7_gsca, specificGeneset=specificGeneset)

## End(Not run)

## Example3: report d7_gsca using a cutoff to filter away edges with small weight
## Not run: 
report(d7_gsca, cutoff = 0.01)

## End(Not run)

## Not run: 
# =================================================================
# NWA class
## load a NWA object(see the examples of analyze NWA for details)
data(d7_nwa)

## report d7_nwa
report(d7_nwa)

## End(Not run)

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