xPierABFheatmap: Function to visualise ABF evidence using heatmap

In Pi: Leveraging Genetic Evidence to Prioritise Drug Targets at the Gene and Pathway Level

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)

Pi documentation built on Nov. 26, 2020, 2:01 a.m.