Mercurial > repos > iuc > raceid_inspectclusters
comparison scripts/cluster.R @ 9:f3eb2291da05 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 82a18e57158136e265a26f27feb40f8dc13437bf
| author | iuc |
|---|---|
| date | Wed, 24 Aug 2022 18:11:37 +0000 |
| parents | 41f34e925bd5 |
| children |
comparison
equal
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| 8:2b0d3e2f402a | 9:f3eb2291da05 |
|---|---|
| 1 #!/usr/bin/env R | 1 #!/usr/bin/env R |
| 2 VERSION <- "0.5" # nolint | 2 VERSION <- "0.5" # nolint |
| 3 | 3 |
| 4 args <- commandArgs(trailingOnly = T) | 4 args <- commandArgs(trailingOnly = TRUE) |
| 5 | 5 |
| 6 if (length(args) != 1) { | 6 if (length(args) != 1) { |
| 7 message(paste("VERSION:", VERSION)) | 7 message(paste("VERSION:", VERSION)) |
| 8 stop("Please provide the config file") | 8 stop("Please provide the config file") |
| 9 } | 9 } |
| 50 } | 50 } |
| 51 | 51 |
| 52 if (filt.use.ccorrect) { | 52 if (filt.use.ccorrect) { |
| 53 par(mfrow = c(2, 2)) | 53 par(mfrow = c(2, 2)) |
| 54 sc <- do.call(CCcorrect, c(sc, filt.ccc)) | 54 sc <- do.call(CCcorrect, c(sc, filt.ccc)) |
| 55 print(plotdimsat(sc, change = T)) | 55 print(plotdimsat(sc, change = TRUE)) |
| 56 print(plotdimsat(sc, change = F)) | 56 print(plotdimsat(sc, change = FALSE)) |
| 57 } | 57 } |
| 58 return(sc) | 58 return(sc) |
| 59 } | 59 } |
| 60 | 60 |
| 61 do.cluster <- function(sc) { # nolint | 61 do.cluster <- function(sc) { # nolint |
| 62 sc <- do.call(compdist, c(sc, clust.compdist)) | 62 sc <- do.call(compdist, c(sc, clust.compdist)) |
| 63 sc <- do.call(clustexp, c(sc, clust.clustexp)) | 63 sc <- do.call(clustexp, c(sc, clust.clustexp)) |
| 64 if (clust.clustexp$sat) { | 64 if (clust.clustexp$sat) { |
| 65 print(plotsaturation(sc, disp = F)) | 65 print(plotsaturation(sc, disp = FALSE)) |
| 66 print(plotsaturation(sc, disp = T)) | 66 print(plotsaturation(sc, disp = TRUE)) |
| 67 } | 67 } |
| 68 print(plotjaccard(sc)) | 68 print(plotjaccard(sc)) |
| 69 return(sc) | 69 return(sc) |
| 70 } | 70 } |
| 71 | 71 |
| 123 print(do.call(mtext, c(paste(buffer, "Sig. Genes"), test))) | 123 print(do.call(mtext, c(paste(buffer, "Sig. Genes"), test))) |
| 124 test$line <- 0 | 124 test$line <- 0 |
| 125 print(do.call(mtext, c(paste(buffer, "(fc > ", | 125 print(do.call(mtext, c(paste(buffer, "(fc > ", |
| 126 genelist.foldchange, ")"), test))) | 126 genelist.foldchange, ")"), test))) |
| 127 }) | 127 }) |
| 128 write.table(df, file = out.genelist, sep = "\t", quote = F) | 128 write.table(df, file = out.genelist, sep = "\t", quote = FALSE) |
| 129 } | 129 } |
| 130 | 130 |
| 131 | 131 |
| 132 writecellassignments <- function(sc) { | 132 writecellassignments <- function(sc) { |
| 133 dat <- sc@cluster$kpart | 133 dat <- sc@cluster$kpart |
| 136 cluster.initial = dat, | 136 cluster.initial = dat, |
| 137 cluster.final = sc@cpart, | 137 cluster.final = sc@cpart, |
| 138 is.outlier = names(dat) %in% sc@out$out) | 138 is.outlier = names(dat) %in% sc@out$out) |
| 139 | 139 |
| 140 write.table(tab, file = out.assignments, sep = "\t", | 140 write.table(tab, file = out.assignments, sep = "\t", |
| 141 quote = F, row.names = F) | 141 quote = FALSE, row.names = FALSE) |
| 142 } | 142 } |
| 143 | 143 |
| 144 | 144 |
| 145 pdf(out.pdf) | 145 pdf(out.pdf) |
| 146 | 146 |
| 156 "% of genes remain,", | 156 "% of genes remain,", |
| 157 sprintf("%.1f", 100 * ncol(as.matrix( | 157 sprintf("%.1f", 100 * ncol(as.matrix( |
| 158 getfdata(sc))) / ncol(sc@expdata)), | 158 getfdata(sc))) / ncol(sc@expdata)), |
| 159 "% of cells remain")) | 159 "% of cells remain")) |
| 160 write.table(as.matrix(sc@ndata), file = out.table, col.names = NA, | 160 write.table(as.matrix(sc@ndata), file = out.table, col.names = NA, |
| 161 row.names = T, sep = "\t", quote = F) | 161 row.names = TRUE, sep = "\t", quote = FALSE) |
| 162 } | 162 } |
| 163 | 163 |
| 164 if (use.cluster) { | 164 if (use.cluster) { |
| 165 par(mfrow = c(2, 2)) | 165 par(mfrow = c(2, 2)) |
| 166 sc <- do.cluster(sc) | 166 sc <- do.cluster(sc) |