kinaseSubstrateHeatmap: Kinase-substrate annotation prioritisation heatmap

In PYangLab/PhosR: A set of methods and tools for comprehensive analysis of phosphoproteomics data

Kinase-substrate annotation prioritisation heatmap

Description

Kinase-substrate annotation prioritisation heatmap

Usage

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

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)
    
kinaseSubstrateHeatmap(L6.matrices)
kinaseSubstrateHeatmap(L6.matrices, printPlot=TRUE)

PYangLab/PhosR documentation built on Feb. 3, 2024, 3:29 a.m.