Mercurial > repos > iuc > dropletutils

comparison scripts/dropletutils.Rscript @ 3:f0de368eabca draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit a4cee4cac5097029188d836d5b904b605dbb943d"
author iuc
date Tue, 15 Oct 2019 09:03:56 -0400
parents a8aa294401be
children cdf4443d5625
comparison
equal deleted inserted replaced
2:a8aa294401be 3:f0de368eabca
17 17
18 writeTSV <- function(fileout, obj){ 18 writeTSV <- function(fileout, obj){
19 write.table(as.matrix(obj), file=fileout, col.names=NA, sep='\t', quote=FALSE) 19 write.table(as.matrix(obj), file=fileout, col.names=NA, sep='\t', quote=FALSE)
20 } 20 }
21 21
22 writeOut <- function(counts, fileout, typeout){ 22 determineGeneIDs <- function(object){
23 if (!is.null(rowData(object)$Symbol)){
24 return(rowData(object)$Symbol)
25 }
26 return(rownames(object))
27 }
28
29 getCounts <- function(object){
30 return(Matrix(counts(object), sparse=TRUE))
31 }
32
33 writeOut <- function(object, fileout, typeout){
23 if (typeout == "tsv"){ 34 if (typeout == "tsv"){
24 writeTSV(fileout, counts) 35 writeTSV(fileout, getCounts(object))
25 } 36 }
26 else if (typeout == "h5ad"){ 37 else if (typeout == "h5ad"){
27 write10xCounts(fileout, counts, type="HDF5", overwrite=TRUE) 38 write10xCounts(fileout, getCounts(object),
39 type="HDF5",
40 gene.symbol=determineGeneIDs(object),
41 overwrite=TRUE)
28 } 42 }
29 else if (typeout == "directory"){ 43 else if (typeout == "directory"){
30 write10xCounts(fileout, counts, type="sparse", overwrite=TRUE) 44 write10xCounts(fileout, getCounts(object),
45 type="sparse",
46 gene.symbol=determineGeneIDs(object),
47 overwrite=TRUE)
31 } 48 }
32 } 49 }
33
34 50
35 read10xFiles <- function(filein, typein){ 51 read10xFiles <- function(filein, typein){
36 sce <- NULL 52 sce <- NULL
37 if (typein == "tsv"){ 53 if (typein == "tsv"){
38 ## Exploding memory problems occured here 54 ## Exploding memory problems occured here
90 called <- e.out$is.Cell 106 called <- e.out$is.Cell
91 } 107 }
92 called[is.na(called)] <- FALSE # replace NA's with FALSE 108 called[is.na(called)] <- FALSE # replace NA's with FALSE
93 sce.filtered <- sce[,called] 109 sce.filtered <- sce[,called]
94 110
95 writeOut(counts(sce.filtered), files$out, out.type) 111 writeOut(sce.filtered, files$out, out.type)
96 112
97 message(paste("Cells:", sum(na.omit(e.out$is.Cell)))) 113 message(paste("Cells:", sum(na.omit(e.out$is.Cell))))
98 message(paste("Cells and Limited:", sum(na.omit(e.out$is.CellAndLimited)))) 114 message(paste("Cells and Limited:", sum(na.omit(e.out$is.CellAndLimited))))
99 } 115 }
100 116
106 called <- do.call(defaultDrops, c(dparams)) 122 called <- do.call(defaultDrops, c(dparams))
107 123
108 # Filtered 124 # Filtered
109 sce.filtered <- sce[,called] 125 sce.filtered <- sce[,called]
110 126
111 writeOut(Matrix(counts(sce.filtered),sparse=TRUE), files$out, out.type) 127 writeOut(sce.filtered, files$out, out.type)
112 128
113 message(paste("Cells:", sum(called))) 129 message(paste("Cells:", sum(called)))
114 } 130 }
115 131
116 132