Mercurial > repos > iuc > dropletutils
comparison scripts/generateTestData.Rscript @ 0:4cd9f0008d9c draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
| author | iuc |
|---|---|
| date | Tue, 04 Jun 2019 17:19:52 -0400 |
| parents | |
| children |
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| -1:000000000000 | 0:4cd9f0008d9c |
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| 1 ## | |
| 2 ## conda install bioconductor-dropletutils bioconductor-dnabarcodes | |
| 3 ## | |
| 4 | |
| 5 suppressWarnings(suppressPackageStartupMessages(library(DropletUtils))) | |
| 6 suppressWarnings(suppressPackageStartupMessages(library(DNABarcodes))) | |
| 7 library(Matrix) | |
| 8 | |
| 9 ## Matrix with no column barcodes | |
| 10 set.seed(100) | |
| 11 ##my.counts <- DropletUtils:::simCounts() | |
| 12 my.counts <- DropletUtils:::simCounts(large.rate=0.01, nlarge=500, nsmall=50, nempty=500) | |
| 13 | |
| 14 ## Generate barcodes (size=10, edit=3) and set as headers | |
| 15 barcodes <- create.pool(10) | |
| 16 colnames(my.counts) <- barcodes[1:ncol(my.counts)] | |
| 17 | |
| 18 sce <- SingleCellExperiment(assays = list(counts = as.matrix(my.counts))) | |
| 19 | |
| 20 writeTSV <- function(fileout, obj){ | |
| 21 write.table(as.matrix(obj), file=fileout, col.names=NA, sep='\t', quote=FALSE) | |
| 22 } | |
| 23 | |
| 24 writeOut <- function(counts, fileout, typeout){ | |
| 25 if (typeout == "tsv"){ | |
| 26 writeTSV(fileout, counts) | |
| 27 } | |
| 28 else if (typeout == "h5ad"){ | |
| 29 write10xCounts(fileout, counts, type="HDF5", overwrite=TRUE) | |
| 30 } | |
| 31 else if (typeout == "directory"){ | |
| 32 write10xCounts(fileout, Matrix(counts), type="sparse", overwrite=TRUE) | |
| 33 } | |
| 34 } | |
| 35 | |
| 36 writeOut(Matrix(counts(sce)), "test-data", type="directory") | |
| 37 writeOut(counts(sce), "test-data.h5ad", type="h5ad") | |
| 38 writeOut(counts(sce), "test-data.tsv", type="tsv") |