Mercurial > repos > gaelcge > r_signac_galaxy

annotate signac-LSI.R @ 0:6e0b320d8b6a draft default tip

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