Kinase-substrate annotation prioritisation heatmap

kinaseSubstrateHeatmap(
  phosScoringMatrices,
  top = 3,
  printPlot = NULL,
  filePath = "./kinaseSubstrateHeatmap.pdf",
  width = 10,
  height = 10
)

Arguments

phosScoringMatrices: a matrix returned from kinaseSubstrateScore.
top: the number of top ranked phosphosites for each kinase to be included in the heatmap. Default is 1.
printPlot: indicate whether the plot should be saved as a PDF in the specified directory. Default is NULL, otherwise specify TRUE.
filePath: path name to save the plot as a PDF file. Default saves in the working directory.
width: width of PDF.
height: height of PDF.

Value

a pheatmap object.

Examples

# \donttest{
data('phospho_L6_ratio_pe')
data('SPSs')
data('PhosphoSitePlus')

ppe <- phospho.L6.ratio.pe
sites = paste(sapply(GeneSymbol(ppe), function(x)x),";",
    sapply(Residue(ppe), function(x)x),
    sapply(Site(ppe), function(x)x),
    ";", sep = "")
grps = gsub("_.+", "", colnames(ppe))
design = model.matrix(~ grps - 1)
ctl = which(sites %in% SPSs)
ppe = RUVphospho(ppe, M = design, k = 3, ctl = ctl)

phosphoL6 = SummarizedExperiment::assay(ppe, "normalised")

# filter for up-regulated phosphosites
phosphoL6.mean <- meanAbundance(phosphoL6, grps = grps)
aov <- matANOVA(mat=phosphoL6, grps = grps)
idx <- (aov < 0.05) & (rowSums(phosphoL6.mean > 0.5) > 0)
phosphoL6.reg <- phosphoL6[idx, ,drop = FALSE]

L6.phos.std <- standardise(phosphoL6.reg)

rownames(L6.phos.std) <- paste0(GeneSymbol(ppe), ";", Residue(ppe), 
    Site(ppe), ";")[idx]

L6.phos.seq <- Sequence(ppe)[idx]

L6.matrices <- kinaseSubstrateScore(PhosphoSite.mouse, L6.phos.std,
    L6.phos.seq, numMotif = 5, numSub = 1)
#> Number of kinases passed motif size filtering: 114
#> Number of kinases passed profile size filtering: 44
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#> done.
#> Scoring phosphosites against kinase-substrate profiles:
#> done.
#> Generating combined scores for phosphosites
#> by motifs and phospho profiles:
#> done.

    
kinaseSubstrateHeatmap(L6.matrices)

kinaseSubstrateHeatmap(L6.matrices, printPlot=TRUE)
#> pdf 
#>   3 
# }