xPierABFheatmap {Pi} | R Documentation

## Function to visualise ABF evidence using heatmap

### Description

`xPierABFheatmap` is supposed to visualise ABF evidence using heatmap. It returns an object of class "ggplot".

### Usage

    xPierABFheatmap(
    data,
    xTarget,
    type = c("Gene", "Gene_SNP"),
    colormap = "steelblue-lightyellow-orange",
    zlim = c(-0.5, 0.5)
    )

### Arguments

`data` | an input vector containing gene symbols
`xTarget` | a "dTarget" or "sTarget" object with the componet 'list_pNode' related to 'eGene' predictors. Alternatively, it can be a data frame with columns ('context','mode','probeID','Symbol','gene_cse','snps','snp_cse','A1','A2','b_GWAS','b_eQTL','b_ABF','p_GWAS','p_eQTL','pp_ABF','H4')
`type` | the type of the heatmap. It can be "Gene" (gene-centric heatmap) or "Gene_SNP" (heatmap for the gene-snp pair)
`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), and "rainbow" (rainbow colormap, that is, red-yellow-green-cyan-blue-magenta). Alternatively, any hyphen-separated HTML color names, e.g. "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 z values for which colors should be plotted

### Value

an object of class "ggplot" appended with 'mat' (the matrix colored by 'b_ABF') and 'df' (a data frame with columns 'priority','code','context','mode','ProbeID','Symbol','gene_cse','snps','snp_cse','A1','A2','b_GWAS','b_eQTL','b_ABF','p_GWAS','p_eQTL','pp_ABF','direction_GWAS','direction_eQTL','direction_ABF').

### Note

none

### See Also

`xSparseMatrix`, `xHeatmap`, `xSparseMatrix`

### Examples

    RData.location <- "http://galahad.well.ox.ac.uk/bigdata"
    ## Not run:
    gp <- xPierABFheatmap(data, dTarget)

    ## End(Not run)

[Package Pi version 2.4.0 Index]