xEnrichGGraph | R Documentation

## Function to visualise enrichment results using a ggraph-like lauout

### Description

`xEnrichGGraph` is supposed to visualise enrichment results using a ggraph-like lauout.

### Usage

    xEnrichGGraph(
    eTerm,
    ig = NULL,
    fixed = T,
    node.color = c("zscore", "adjp", "or"),
    colormap = "grey-orange-darkred",
    zlim = NULL,
    node.size = c("adjp", "zscore", "or"),
    slim = NULL,
    node.size.range = c(0.5, 4),
    node.label.size = 2,
    leave = T,
    ncolumns = NULL,
    ...
    )

### Arguments

`eTerm` | an object of class "eTerm" or "ls_eTerm". Alterntively, it can be a data frame having all these columns ('name','adjp','or','zscore'; 'group' optionally)
`ig` | an object of class "igraph" with node attribute 'name'. Note: the node labels would be the node attribute 'name' unless the node attribute 'label' is explicitely provided. If provided, only those terms within it will be visualised. By default, it is NULL meaning no surch restriction
`fixed` | logical to indicate whether all terms in ig will be visualised. By default, it is TURE; otherwise only overlapped terms from eTerm will be visualised
`node.color` | which statistics will be used for node coloring. It can be "or" for the odds ratio, "adjp" for adjusted p value (FDR) and "zscore" for enrichment z-score

`colormap`

short name for the colormap. It can be one of "jet" (jet colormap), "bwr" (blue-white-red colormap), "gbr" (green-black-red colormap), "wyr" (white-yellow-red colormap), "br" (black-red colormap), "yr" (yellow-red colormap), "wb" (white-black colormap), "rainbow" (rainbow colormap, that is, red-yellow-green-cyan-blue-magenta), and "ggplot2" (emulating ggplot2 default color palette). Alternatively, any hyphen-separated HTML color names, e.g. "lightyellow-orange" (by default), "blue-black-yellow", "royalblue-white-sandybrown", "darkgreen-white-darkviolet". A list of standard color names can be found in http://html-color-codes.info/color-names

`zlim` | the minimum and maximum values for which colors should be plotted
`node.size` | which statistics will be used for node size. It can be "or" for the odds ratio, "adjp" for adjusted p value (FDR) and "zscore" for enrichment z-score
`slim` | the minimum and maximum values for which sizes should be plotted
`node.size.range` | the range of actual node size
`node.label.size` | the text size of the node labelings. By default, it is 2. If 0, all labellings will be disabled
`leave` | the logic specifying whether or not only leaves (nodes/labellings) shown. This can be disenabled if the layout does not support tips
`ncolumns` | an integer specifying the number of columns for facet_wrap. By defaul, it is NULL (decided on according to the number of groups that will be visualised)
`...` | additional graphic parameters used in xGGraph

### Value

a ggplot2 object appended with 'ig', 'data' which should contain columns 'x','y', 'name' (the same as V(ig)$name), 'label' (if not given in ig, a 'name' varient), 'data_enrichment' (enrichment results), and 'gp_template' with labelling if multiple groups (together with no labelling for the colored plots).

### Note

none

### See Also

`xGGraph`

### 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"

    # load the atlas of AA pathways
    AA.template <- xRDataLoader("AA.template",
    RData.location=RData.location)
    # consensus tree
    ig <- AA.template$consensus$ig

    # enrichment analysis using AA pathways
    input <- xRDataLoader('Haploid_regulators_all',
    RData.location=RData.location)
    data <- subset(input, Phenotype=="AKT")
    genes <- data$Gene[data$FDR<0.05]
    background <- data$Gene
    eTerm <- xEnricherGenes(genes, background=background, ontology="AA",
    min.overlap=5, test="fisher", RData.location=RData.location)

    # circular visualisation of enriched AA pathways
    gp <- xEnrichGGraph(eTerm, ig)

    ###############################
    # advanced use: multiple groups
    # enrichment analysis using AA pathways
    Haploid <- subset(input, FDR<0.05)
    ls_group <- split(x=Haploid$Gene, f=Haploid$Phenotype)
    background <- unique(input$Gene)
    ls_eTerm <- xEnricherGenesAdv(ls_group, background=background,
    ontologies="AA", test="fisher", min.overlap=5,
    RData.location=RData.location)

    # circular visualisation of enriched AA pathways
    gp <- xEnrichGGraph(ls_eTerm, ig)
    gp
    gp$gp_template

    ## End(Not run)