In C3BI-pasteur-fr/UTechSCB-SCHNAPPs: Single Cell Shiny Application for Analysing Single Cell Transcriptomics Data

require(psychTools)

load("~/Downloads/pHeatMap_data/sessionData.RData")

     if (is.null(scale)) {
      heatmapData$scale = "none"
    } else {
      heatmapData$scale = "row"
    }
    if (length(addColNames) > 0 & moreOptions) {
        heatmapData$annotation_col <- proje[rownames(heatmapData$annotation_col), addColNames, drop = FALSE]
      }
      if (sum(orderColNames %in% colnames(proje)) > 0 & moreOptions) {
        heatmapData$cluster_cols <- FALSE
        colN <- rownames(dfOrder(proje, orderColNames))
        colN <- colN[colN %in% colnames(heatmapData$mat)]
        heatmapData$mat <- heatmapData$mat[, colN, drop = FALSE]
      }
do.call(TRONCO::pheatmap, heatmapData)

library("PerformanceAnalytics")
chart.Correlation(heatmapData$mat, histogram=TRUE, pch=19)

library("Hmisc")
colnames(heatmapData$mat)
rownames(proje)
colnames(proje)
nums <- unlist(lapply(proje, is.numeric))
numProje = proje[,nums]
colnames(numProje)

numProje <- t(numProje)[,colnames(heatmapData$mat)]
rownames(numProje)
corrInput <- as.matrix(rbind(numProje,heatmapData$mat))
rownames(corrInput)
res2 <- rcorr(t(corrInput))
# res2
sum(rownames(res2$P) %in% colnames(proje[, nums]))
# ++++++++++++++++++++++++++++
# flattenCorrMatrix
# ++++++++++++++++++++++++++++
# cormat : matrix of the correlation coefficients
# pmat : matrix of the correlation p-values
flattenCorrMatrix <- function(cormat, pmat) {
  ut <- upper.tri(cormat)
  data.frame(
    row = rownames(cormat)[row(cormat)[ut]],
    column = rownames(cormat)[col(cormat)[ut]],
    cor  =(cormat)[ut],
    p = pmat[ut]
    )
}
cormat = res2$r
pmat = res2$P
ut <- upper.tri(upper.tri(res2$r))


flatMat <- flattenCorrMatrix(res2$r, res2$P)
flatMat[flatMat$column %in% colnames(proje[, nums]) & 
        (!flatMat$row %in% colnames(proje[, nums]))  , ]
flatMat = flatMat[order(flatMat$cor, decreasing = F),]
DT::datatable(flatMat[flatMat$row == "PC5" &
                        flatMat$p < 0.005,])

C3BI-pasteur-fr/UTechSCB-SCHNAPPs documentation built on April 23, 2024, 11:54 a.m.