Mercurial > repos > iuc > raceid_inspecttrajectory
comparison scripts/cluster.R @ 4:86e2358cf273 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
author | iuc |
---|---|
date | Mon, 12 Aug 2019 13:03:03 -0400 |
parents | 4164c0da0a5d |
children | c8434a623268 |
comparison
equal
deleted
inserted
replaced
3:4164c0da0a5d | 4:86e2358cf273 |
---|---|
1 #!/usr/bin/env R | 1 #!/usr/bin/env R |
2 VERSION = "0.4" | 2 VERSION = "0.5" |
3 | 3 |
4 args = commandArgs(trailingOnly = T) | 4 args = commandArgs(trailingOnly = T) |
5 | 5 |
6 if (length(args) != 1){ | 6 if (length(args) != 1){ |
7 message(paste("VERSION:", VERSION)) | 7 message(paste("VERSION:", VERSION)) |
137 | 137 |
138 }) | 138 }) |
139 write.table(df, file=out.genelist, sep="\t", quote=F) | 139 write.table(df, file=out.genelist, sep="\t", quote=F) |
140 } | 140 } |
141 | 141 |
142 | |
143 writecellassignments <- function(sc){ | |
144 dat <- sc@cluster$kpart | |
145 tab <- data.frame(row.names = NULL, | |
146 cells = names(dat), | |
147 cluster.initial = dat, | |
148 cluster.final = sc@cpart, | |
149 is.outlier = names(dat) %in% sc@out$out) | |
150 | |
151 write.table(tab, file=out.assignments, sep="\t", quote=F, row.names = F) | |
152 } | |
153 | |
154 | |
142 pdf(out.pdf) | 155 pdf(out.pdf) |
143 | 156 |
144 if (use.filtnormconf){ | 157 if (use.filtnormconf){ |
145 sc <- do.filter(sc) | 158 sc <- do.filter(sc) |
146 message(paste(" - Source:: genes:",nrow(sc@expdata),", cells:",ncol(sc@expdata))) | 159 message(paste(" - Source:: genes:",nrow(sc@expdata),", cells:",ncol(sc@expdata))) |
147 message(paste(" - Filter:: genes:",nrow(getfdata(sc)),", cells:",ncol(getfdata(sc)))) | 160 message(paste(" - Filter:: genes:",nrow(getfdata(sc)),", cells:",ncol(getfdata(sc)))) |
148 message(paste(" :: ", | 161 message(paste(" :: ", |
149 sprintf("%.1f", 100 * nrow(getfdata(sc))/nrow(sc@expdata)), "% of genes remain,", | 162 sprintf("%.1f", 100 * nrow(getfdata(sc))/nrow(sc@expdata)), "% of genes remain,", |
150 sprintf("%.1f", 100 * ncol(getfdata(sc))/ncol(sc@expdata)), "% of cells remain")) | 163 sprintf("%.1f", 100 * ncol(getfdata(sc))/ncol(sc@expdata)), "% of cells remain")) |
164 write.table(as.matrix(sc@ndata), file=out.table, col.names=NA, row.names=T, sep="\t", quote=F) | |
151 } | 165 } |
152 | 166 |
153 if (use.cluster){ | 167 if (use.cluster){ |
154 par(mfrow=c(2,2)) | 168 par(mfrow=c(2,2)) |
155 sc <- do.cluster(sc) | 169 sc <- do.cluster(sc) |
159 | 173 |
160 par(mfrow=c(2,2), mar=c(1,1,6,1)) | 174 par(mfrow=c(2,2), mar=c(1,1,6,1)) |
161 sc <- do.clustmap(sc) | 175 sc <- do.clustmap(sc) |
162 | 176 |
163 mkgenelist(sc) | 177 mkgenelist(sc) |
178 writecellassignments(sc) | |
164 } | 179 } |
165 | 180 |
166 dev.off() | 181 dev.off() |
167 | 182 |
168 saveRDS(sc, out.rdat) | 183 saveRDS(sc, out.rdat) |