Created
August 6, 2024 16:56
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simple collection of matrix.mtx and parquet assets from Xenium exemplary dataset
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| # retrieve these from https://mghp.osn.xsede.org/bir190004-bucket01/BiocXenData/ | |
| #-rw-r--r-- 1 exouser exouser 3300521324 Mar 20 21:17 transcripts.parquet | |
| #-rw-r--r-- 1 exouser exouser 68454210 Mar 20 21:16 nucleus_boundaries.parquet | |
| #-rw-r--r-- 1 exouser exouser 73791358 Mar 20 21:15 cell_boundaries.parquet | |
| #-rw-r--r-- 1 exouser exouser 242459483 Apr 10 03:46 cell_feature_matrix.tar.gz | |
| #-rw-r--r-- 1 exouser exouser 44907408 Mar 20 21:15 cells.csv.gz | |
| # tar zxf cell_feature_matrix.tar.gz to obtain folder cell_feature_matrix | |
| library(Matrix) | |
| library(SingleCellExperiment) | |
| library(ParquetDataFrame) # from github.com/LTLA/ParquetDataFrame | |
| counts = readMM("cell_feature_matrix/matrix.mtx.gz") | |
| barc = read.delim("cell_feature_matrix/barcodes.tsv.gz", sep="\t", h=FALSE) | |
| fea = read.delim("cell_feature_matrix/features.tsv.gz", h=FALSE, sep="\t") | |
| cellmeta = read.csv("cells.csv.gz") | |
| rownames(counts) = fea$V1 | |
| colnames(counts) = barc$V1 | |
| sce = SingleCellExperiment(assays=SimpleList(counts=counts)) | |
| colnames(fea) = c("ensid", "symbol", "type") | |
| rowData(sce) = DataFrame(fea) | |
| colData(sce) = DataFrame(cellmeta) | |
| tx = ParquetDataFrame("transcripts.parquet") | |
| cellb = ParquetDataFrame("cell_boundaries.parquet") | |
| nucb = ParquetDataFrame("nucleus_boundaries.parquet") | |
| setClass("XenSCE", contains="SingleCellExperiment", slots=c(cellbounds="ParquetDataFrame", | |
| transcripts="ParquetDataFrame", nucbounds="ParquetDataFrame")) | |
| setMethod("show", "XenSCE", function(object) { | |
| callNextMethod(); | |
| cat("Parquet elements:\n") | |
| print(xdims(object)) | |
| } ) | |
| #' helper function for XenSCE show method | |
| xdims = function (x) | |
| { | |
| ans = sapply(c("transcripts", "cellbounds", "nucbounds"), | |
| function(z) dim(slot(x, z))) | |
| ans = t(ans) | |
| colnames(ans) = c("nrow", "ncol") | |
| data.frame(ans) | |
| } | |
| #' method for transcript extraction | |
| #' @export | |
| setGeneric("getTranscripts", function(x) standardGeneric("getTranscripts")) | |
| setMethod("getTranscripts", "XenSCE", function(x) slot(x, "transcripts")) | |
| #' method for cell boundary extraction | |
| #' @export | |
| setGeneric("getCellBoundaries", function(x) standardGeneric("getCellBoundaries")) | |
| setMethod("getCellBoundaries", "XenSCE", function(x) slot(x, "cellbounds")) | |
| #' method for nucleus boundary extraction | |
| #' @export | |
| setGeneric("getNucleusBoundaries", function(x) standardGeneric("getNucleusBoundaries")) | |
| setMethod("getNucleusBoundaries", "XenSCE", function(x) slot(x, "nucbounds")) | |
| myxen = new("XenSCE", sce, transcripts=tx, cellbounds=cellb, nucbounds=nucb) | |
| myxen |
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