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Original identities not respected in ATAC analysis #117

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Original identities not respected in ATAC analysis #117

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11 changes: 8 additions & 3 deletions R/ATACRunSeurat.R
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Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,7 @@
#' for example "chr10_100020591_100020841".
#' @param type Type of the input matrix. Default is "matrix". Set to "object" if the input is Seurat object.
#' @param project Output project name. Default is "MAESTRO.scATAC.Seurat".
#' @param orign.ident Orginal identity for the input cells. If supplied, should keep the same order with the column name of the peak x cell matrix.
#' @param orig.ident Orginal identity for the input cells. If supplied, should keep the same order with the column name of the peak x cell matrix.
#' @param method Methods for dimension reduction, available options are LSI and PCA. Default is "LSI".
#' @param min.c Minimum number of cells required for a peak. Will exclude the peaks from input matrix if they only identified in
#' less than \code{min.c} cells. Default is 10. See \code{\link{CreateSeuratObject}} for details.
Expand Down Expand Up @@ -48,7 +48,7 @@
#' @importFrom Gmisc fastDoCall
#' @export

ATACRunSeurat <- function(inputMat, type = "matrix", project = "MAESTRO.scATAC.Seurat", orign.ident = NULL,
ATACRunSeurat <- function(inputMat, type = "matrix", project = "MAESTRO.scATAC.Seurat", orig.ident = NULL,
min.c = 10, min.p = 100, method = "LSI", dims.use = 1:30,
cluster.res = 0.6, only.pos = FALSE, peaks.test.use = "presto",
peaks.cutoff = 1E-5, peaks.pct = 0.1, peaks.logfc = 0.2,
Expand Down Expand Up @@ -106,7 +106,12 @@ ATACRunSeurat <- function(inputMat, type = "matrix", project = "MAESTRO.scATAC.S
# SeuratObj <- FindClusters(object = SeuratObj, resolution = res)
p3 <- DimPlot(object = SeuratObj, pt.size = 0.5, label = TRUE)
ggsave(file.path(paste0(project, "_cluster.png")), p3, width=5, height=4)

if(!is.null(orig.ident)){
SeuratObj$orig.ident <- orig.ident
p4 = DimPlot(object = SeuratObj, label = TRUE, pt.size = 0.2, group.by = "orig.ident", label.size = 3)
ggsave(file.path(paste0(SeuratObj@project.name, "_original.png")), p4, width=5, height=4)
}

#============ DE analysis ============
message("Identify cluster specific peaks ...")
cluster.peaks <- NULL
Expand Down