support Seurat v3.0

library(RColorBrewer)

library(scales)

library(tclust)

library(Seurat) # V2.3.0

library(Seurat)

getDAregion <- function(

  X, cell.idx, k, alpha, restr.fact = 50,

  cell.labels, labels.1, labels.2, 

  do.plot = T, plot.embedding = NULL, size = 0.5

  do.plot = T, plot.embedding = NULL, size = 0.5, 

  ...

){

  X.tclust <- runtclust(X, cell.idx, k, alpha, restr.fact)

  X.tclust <- runtclust(X, cell.idx, k, alpha, restr.fact, ...)

  X.n.da <- length(unique(X.tclust)) - 1

  X.da.stat <- matrix(0, nrow = X.n.da, ncol = 3)

  colnames(X.da.stat) <- c("DA.score","pval.wilcoxon","pval.ttest")

#' @param cell.idx result "da.cell.idx" from the output of function getDAcells

#' @param da.region.label result "cluster.res" from the output of function getDAregion

#' @param obj Seurat object that contain ALL cells in the analysis

#' @param version Seurat version of 'obj', default is '2', support '2' or '3'

#' @param ... parameters for Seurat function FindMarkers()

#' 

#' @return a list of matrices with markers for each DA region

findMarkersForDAregion <- function(

  cell.idx, da.region.label, obj, ...

  cell.idx, da.region.label, obj, version = "2", ...

){

  if(!version %in% c("2","3")){

    stop("Parameter version can only be '2' or '3'!")

  }

  n.da <- length(unique(da.region.label)) - 1

  obj@meta.data$da <- 0

  obj@meta.data$da[cell.idx] <- da.region.label

  if(version == "2"){

    obj <- SetAllIdent(obj, id = "da")

  } else if (version == "3"){

    Idents(obj) <- obj@meta.data$da

  }

  da.markers <- list()

  for(ii in 1:n.da){

# get DA regions with tclust

runtclust <- function(X, cell.idx, k, alpha, restr.fact = 50){

runtclust <- function(X, cell.idx, k, alpha, restr.fact = 50, ...){

  X.tclust.res <- tclust(

    x = X[cell.idx,], k = k, alpha = alpha, restr.fact = restr.fact

    x = X[cell.idx,], k = k, alpha = alpha, restr.fact = restr.fact, ...

  )

  return(X.tclust.res$cluster)