Mercurial > repos > gaelcge > r_signac_galaxy

annotate signac-dimplot.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("--dims"),
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23 action = "store",
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24 type = 'character',
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25 help = "Dimension for x-axis (default 1)"
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26 ),
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27 make_option(
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28 c("-p", "--pt-size"),
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29 action = "store",
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30 default = 1,
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31 type = 'integer',
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32 help = "Adjust point size for plotting"
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33 ),
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34 make_option(
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35 c("-l", "--label-size"),
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36 action = "store",
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37 default = 4,
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38 type = 'integer',
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39 help = "Sets size of labels."
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40 ),
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41 make_option(
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42 c("-d", "--do-label"),
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43 action = "store",
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44 default = FALSE,
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45 type = 'logical',
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46 help = "Whether to label the clusters."
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47 ),
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48 make_option(
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49 c("--group-by"),
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50 action = "store",
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51 default = 'ident',
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52 type = 'character',
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53 help = "Group (color) cells in different ways (for example, orig.ident)."
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54 ),
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55 make_option(
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56 c("--png-width"),
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57 action = "store",
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58 default = 1000,
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59 type = 'integer',
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60 help = "Width of png (px)."
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61 ),
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62 make_option(
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63 c("--png-height"),
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64 action = "store",
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65 default = 1000,
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66 type = 'integer',
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67 help = "Height of png file (px)."
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68 ),
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69 make_option(
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70 c("--output_image_file"),
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71 action = "store",
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72 default = NA,
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73 type = 'character',
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74 help = "File name in which to store serialized R matrix object."
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75 )
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76 )
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77
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78 opt <- wsc_parse_args(option_list)
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79
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80 suppressPackageStartupMessages(require(Seurat))
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81 suppressPackageStartupMessages(require(Signac))
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82
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83 set.seed(1234)
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84
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85 dims_use <- opt$dims
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86 if ( ! is.null(dims_use)){
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87 dims_parsed <- wsc_parse_numeric(opt, 'dims')
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88 dims_use <- seq(from = dims_parsed[1], to = dims_parsed[2])
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89 }
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90
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91 # extract gene annotations from EnsDb
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92 signac_object <- readRDS(file = opt$signac_object)
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93
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94 png(filename = opt$output_image_file, width = opt$png_width, height = opt$png_height)
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95 DimPlot(object = signac_object, dims = dims_use, pt.size = opt$pt_size, label.size = opt$label_size, group.by = opt$group_by) + NoLegend()
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96 dev.off()