xEnrichCompare | R Documentation

## Function to compare enrichment results using side-by-side barplots

### Description

`xEnrichCompare` is supposed to compare enrichment results using side-by-side barplots. It returns an object of class "ggplot".

### Usage

    xEnrichCompare(
    list_eTerm,
    displayBy = c("fc", "adjp", "fdr", "zscore", "pvalue"),
    FDR.cutoff = 0.05,
    bar.label = TRUE,
    bar.label.size = 2.5,
    wrap.width = NULL,
    sharings = NULL,
    font.family = "sans",
    facet = TRUE,
    signature = TRUE
    )

### Arguments

`list_eTerm` | a list of "eTerm" objects
`displayBy` | which statistics will be used for comparison. It can be "fc" for enrichment fold change (by default), "adjp" or "fdr" for adjusted p value (or FDR), "pvalue" for p value, "zscore" for enrichment z-score
`FDR.cutoff` | FDR cutoff used to declare the significant terms. By default, it is set to 0.05
`bar.label` | logical to indicate whether to label each bar with FDR. By default, it sets to true for bar labelling
`bar.label.size` | an integer specifying the bar labelling text size. By default, it sets to 3
`wrap.width` | a positive integer specifying wrap width of name
`sharings` | a numeric vector specifying whether only shared terms will be displayed. For example, when comparing three groups of enrichment results, it can be set into c(2,3) to display only shared terms by any two or all three. By default, it is NULL meaning no such restriction
`font.family` | the font family for texts
`facet` | logical to indicate whether to facet/wrap a 1d of panels into 2d. By default, it sets TRUE
`signature` | logical to indicate whether the signature is assigned to the plot caption. By default, it sets TRUE showing which function is used to draw this graph

### Value

an object of class "ggplot", but appended with a 'g' (an igraph object to represent DAG after being unionised)

### Note

none

### See Also

`xEnricherGenes`, `xEnricherSNPs`, `xEnrichDAGplotAdv`

### Examples

    ## Not run:
    # Load the XGR package and specify the location of built-in data
    library(XGR)
    RData.location <- "http://galahad.well.ox.ac.uk/bigdata/"

    # 1) load eQTL mapping results: cis-eQTLs significantly induced by IFN
    cis <- xRDataLoader(RData.customised='JKscience_TS2A',
    RData.location=RData.location)
    ind <- which(cis$IFN_t > 0 & cis$IFN_fdr < 0.05)
    df_cis <- cis[ind, c('variant','Symbol','IFN_t','IFN_fdr')]
    data <- df_cis$variant

    # 2) Enrichment analysis using Experimental Factor Ontology (EFO)
    # 2a) Without considering LD SNPs and without respecting ontology tree
    eTerm_noLD_noTree <- xEnricherSNPs(data, ontology="EF_disease",
    include.LD=NA, ontology.algorithm="none",
    RData.location=RData.location)
    # 2b) Without considering LD SNPs but respecting ontology tree
    eTerm_noLD_Tree <- xEnricherSNPs(data, ontology="EF_disease",
    include.LD=NA, ontology.algorithm="lea", RData.location=RData.location)
    # 2c) Considering LD SNPs but without respecting ontology tree
    eTerm_LD_noTree <- xEnricherSNPs(data, ontology="EF_disease",
    include.LD="EUR", LD.r2=0.8, ontology.algorithm="none",
    RData.location=RData.location)
    # 2d) Considering LD SNPs and respecting ontology tree
    eTerm_LD_Tree <- xEnricherSNPs(data, ontology="EF_disease",
    include.LD="EUR", LD.r2=0.8, ontology.algorithm="lea",
    RData.location=RData.location)

    # 3) Compare enrichment results
    list_eTerm <- list(eTerm_noLD_noTree, eTerm_noLD_Tree, eTerm_LD_noTree,
    eTerm_LD_Tree)
    names(list_eTerm) <- c('LD(-) & Tree(-)','LD(-) & Tree(+)','LD(+) &
    Tree(-)','LD(+) & Tree(+)')
    ## side-by-side comparisons
    bp <- xEnrichCompare(list_eTerm, displayBy="fc")
    #pdf(file="enrichment_compared.pdf", height=6, width=12, compress=TRUE)
    print(bp)
    #dev.off()
    ## modify y axis text
    bp + theme(axis.text.y=element_text(size=10,color="black"))
    ## modify x axis title
    bp + theme(axis.title.x=element_text(color="black"))
    ## modify fill colors
    bp + scale_fill_manual(values=c("black","#888888"))
    ## show legend title but hide strip
    bp + theme(legend.position="right", strip.text=element_blank())

    # 4) DAGplot of comparative enrichment results in the context of ontology tree
    xEnrichDAGplotAdv(bp, graph.node.attrs=list(fontsize=100))

    ## End(Not run)