xEnrichBarplot | R Documentation

## Function to visualise enrichment results using a barplot

### Description

`xEnrichBarplot` is supposed to visualise enrichment results using a barplot. It returns an object of class "ggplot".

### Usage

    xEnrichBarplot(eTerm, top_num = 10, displayBy = c("fc", "adjp", "fdr",
    "zscore", "pvalue"), FDR.cutoff = 0.05, bar.label = TRUE,
    bar.label.size = 3, bar.color = "lightyellow-orange", bar.width = 0.8,
    wrap.width = NULL, font.family = "sans", signature = TRUE)

### Arguments

`eTerm` | an object of class "eTerm"
`top_num` | the number of the top terms (sorted according to FDR or adjusted p-values). If it is 'auto', only the significant terms (see below FDR.cutoff) will be displayed
`displayBy` | which statistics will be used for displaying. 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. This option only works when setting top_num (see above) is 'auto'
`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
`bar.color` | either NULL or fill color names ('lightyellow-orange' by default)
`bar.width` | bar width. By default, 80 data
`wrap.width` | a positive integer specifying wrap width of name
`font.family` | the font family for texts
`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"

### Note

none

### See Also

`xEnricherGenes`, `xEnricherSNPs`, `xEnrichViewer`

### 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_dev/"

    # 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)
    # Considering LD SNPs and respecting ontology tree
    eTerm <- xEnricherSNPs(data, ontology="EF", include.LD="EUR",
    LD.r2=0.8, ontology.algorithm="lea", RData.location=RData.location)

    # 3) Barplot of enrichment results
    bp <- xEnrichBarplot(eTerm, top_num="auto", displayBy="fc")
    #pdf(file="enrichment_barplot.pdf", height=6, width=12, compress=TRUE)
    print(bp)
    #dev.off()

    ## End(Not run)

    # 4) use font family (Arial)
    ## Not run:
    source("http://bioconductor.org/biocLite.R"); biocLite("extrafont")
    library(extrafont)
    font_import()
    fonttable()
    ## creating PDF files with fonts
    library(extrafont)
    loadfonts()
    bp <- xEnrichBarplot(eTerm, top_num="auto", displayBy="fc",
    font.family="Arial Black")
    pdf(file="enrichment_barplot_fonts.pdf", height=6, width=12,
    family="Arial Black")
    print(bp)
    dev.off()

    ## End(Not run)