Mercurial > repos > gaelcge > r_signac_galaxy
comparison signac-LSI.R @ 0:6e0b320d8b6a draft default tip
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
| author | gaelcge |
|---|---|
| date | Tue, 02 Aug 2022 19:11:27 +0000 |
| parents | |
| children |
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| -1:000000000000 | 0:6e0b320d8b6a |
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| 1 #!/usr/bin/env Rscript | |
| 2 | |
| 3 # Load optparse we need to check inputs | |
| 4 | |
| 5 suppressPackageStartupMessages(require(optparse)) | |
| 6 | |
| 7 # Load common functions | |
| 8 | |
| 9 suppressPackageStartupMessages(require(workflowscriptscommon)) | |
| 10 | |
| 11 # parse options | |
| 12 | |
| 13 option_list = list( | |
| 14 make_option( | |
| 15 c("--signac-object"), | |
| 16 action = "store", | |
| 17 default = NA, | |
| 18 type = 'character', | |
| 19 help = "" | |
| 20 ), | |
| 21 make_option( | |
| 22 c("--min-cutoff"), | |
| 23 action = "store", | |
| 24 default = NA, | |
| 25 type = 'character', | |
| 26 help = "" | |
| 27 ), | |
| 28 make_option( | |
| 29 c("--output-depthcor"), | |
| 30 action = "store", | |
| 31 default = NA, | |
| 32 type = 'character', | |
| 33 help = "TSS output plot." | |
| 34 ), | |
| 35 make_option( | |
| 36 c("-w", "--png-width"), | |
| 37 action = "store", | |
| 38 default = 1000, | |
| 39 type = 'integer', | |
| 40 help = "Width of png (px)." | |
| 41 ), | |
| 42 make_option( | |
| 43 c("-j", "--png-height"), | |
| 44 action = "store", | |
| 45 default = 1000, | |
| 46 type = 'integer', | |
| 47 help = "Height of png file (px)." | |
| 48 ), | |
| 49 make_option( | |
| 50 c("--output-object-file"), | |
| 51 action = "store", | |
| 52 default = NA, | |
| 53 type = 'character', | |
| 54 help = "File name in which to store serialized R matrix object." | |
| 55 ) | |
| 56 ) | |
| 57 | |
| 58 opt <- wsc_parse_args(option_list) | |
| 59 | |
| 60 suppressPackageStartupMessages(require(Signac)) | |
| 61 | |
| 62 set.seed(1234) | |
| 63 | |
| 64 # extract gene annotations from EnsDb | |
| 65 signac_object <- readRDS(file = opt$signac_object) | |
| 66 | |
| 67 | |
| 68 signac_object <- RunTFIDF(signac_object) | |
| 69 signac_object <- FindTopFeatures(signac_object, min.cutoff = opt$min_cutoff) | |
| 70 signac_object <- RunSVD(signac_object) | |
| 71 | |
| 72 ## Plot the Depth correlation plot | |
| 73 png(filename = opt$output_depthcor, width = opt$png_width, height = opt$png_height) | |
| 74 DepthCor(signac_object) | |
| 75 dev.off() | |
| 76 | |
| 77 # Output to a serialized R object | |
| 78 saveRDS(signac_object, file = opt$output_object_file) |