xPierABFheatmap | R Documentation |
xPierABFheatmap
is supposed to visualise ABF evidence using
heatmap. It returns an object of class "ggplot".
xPierABFheatmap(data, xTarget, type = c("Gene", "Gene_SNP"), colormap = "steelblue-lightyellow-orange", zlim = c(-0.5, 0.5))
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 |
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').
none
xPierABFheatmap
## Not run: # Load the library library(Pi) RData.location <- "http://galahad.well.ox.ac.uk/bigdata/" gp <- xPierABFheatmap(data, dTarget) ## End(Not run)