Mercurial > repos > artbio > gsc_high_dimensions_visualisation

annotate high_dim_visu.R @ 9:58aa18e1fe14 draft default tip

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization commit 7343be2d3b1b8cb1ba0c4c55767b60dbce8f8b22
author artbio
date Thu, 07 Nov 2024 22:43:01 +0000
parents fe6f76030168
children
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9
58aa18e1fe14 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization commit 7343be2d3b1b8cb1ba0c4c55767b60dbce8f8b22
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1 options(
58aa18e1fe14 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization commit 7343be2d3b1b8cb1ba0c4c55767b60dbce8f8b22
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2 show.error.messages = FALSE,
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3 error = function() {
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4 cat(geterrmessage(), file = stderr())
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5 q("no", 1, FALSE)
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6 }
7
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7 )
0
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8 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
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9 warnings()
8
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10
0
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11 library(optparse)
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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12 library(FactoMineR)
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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13 library(factoextra)
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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14 library(Rtsne)
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15 library(ggplot2)
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16 library(ggfortify)
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17 library(RColorBrewer)
4
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18 library(ClusterR)
5
569334568afa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1b98c85982a2a9f9df4b318f672b9b68cff66a93"
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19 library(data.table)
7
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20 library(Polychrome)
0
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21
7
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22 option_list <- list(
9
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23 make_option(
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24 "--data",
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25 default = NA,
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26 type = "character",
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27 help = "Input file that contains expression value to visualise"
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28 ),
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29 make_option(
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30 "--labels",
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31 default = FALSE,
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32 type = "logical",
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33 help = "add labels in scatter plots [default : '%default' ]"
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34 ),
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35 make_option(
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36 "--factor",
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37 default = "",
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38 type = "character",
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39 help = "A two column table that specifies factor levels for contrasting data [default : '%default' ]"
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40 ),
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41 make_option(
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42 "--visu_choice",
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43 default = "PCA",
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44 type = "character",
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45 help = "visualisation method ('PCA', 'tSNE', 'HCPC') [default : '%default' ]"
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46 ),
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47 make_option(
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48 "--Rtsne_seed",
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49 default = 42,
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50 type = "integer",
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51 help = "Seed value for reproducibility [default : '%default' ]"
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52 ),
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53 make_option(
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54 "--Rtsne_dims",
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55 default = 2,
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56 type = "integer",
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57 help = "Output dimensionality [default : '%default' ]"
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58 ),
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59 make_option(
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60 "--Rtsne_initial_dims",
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61 default = 50,
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62 type = "integer",
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63 help = "The number of dimensions that should be retained in the initial PCA step [default : '%default' ]"
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64 ),
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65 make_option(
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66 "--Rtsne_perplexity",
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67 default = 5.0,
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68 type = "numeric",
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69 help = "perplexity [default : '%default' ]"
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70 ),
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71 make_option(
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72 "--Rtsne_theta",
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73 default = 1.0,
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74 type = "numeric",
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75 help = "theta [default : '%default' ]"
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76 ),
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77 make_option(
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78 "--Rtsne_max_iter",
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79 default = 1000,
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80 type = "integer",
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81 help = "max_iter [default : '%default' ]"
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82 ),
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83 make_option(
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84 "--Rtsne_pca",
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85 default = TRUE,
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artbio
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86 type = "logical",
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artbio
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87 help = "Whether an initial PCA step should be performed [default : '%default' ]"
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artbio
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diff changeset
88 ),
58aa18e1fe14 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization commit 7343be2d3b1b8cb1ba0c4c55767b60dbce8f8b22
artbio
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diff changeset
89 make_option(
58aa18e1fe14 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization commit 7343be2d3b1b8cb1ba0c4c55767b60dbce8f8b22
artbio
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90 "--Rtsne_pca_center",
58aa18e1fe14 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization commit 7343be2d3b1b8cb1ba0c4c55767b60dbce8f8b22
artbio
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91 default = TRUE,
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artbio
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92 type = "logical",
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artbio
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93 help = "Should data be centered before pca is applied? [default : '%default' ]"
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artbio
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94 ),
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artbio
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diff changeset
95 make_option(
58aa18e1fe14 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization commit 7343be2d3b1b8cb1ba0c4c55767b60dbce8f8b22
artbio
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96 "--Rtsne_pca_scale",
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artbio
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97 default = FALSE,
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artbio
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98 type = "logical",
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artbio
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99 help = "Should data be scaled before pca is applied? [default : '%default' ]"
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artbio
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100 ),
58aa18e1fe14 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization commit 7343be2d3b1b8cb1ba0c4c55767b60dbce8f8b22
artbio
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101 make_option(
58aa18e1fe14 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization commit 7343be2d3b1b8cb1ba0c4c55767b60dbce8f8b22
artbio
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102 "--Rtsne_normalize",
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artbio
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103 default = TRUE,
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artbio
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104 type = "logical",
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artbio
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105 help = "Should data be normalized internally prior to distance calculations? [default : '%default' ]"
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artbio
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106 ),
58aa18e1fe14 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization commit 7343be2d3b1b8cb1ba0c4c55767b60dbce8f8b22
artbio
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107 make_option(
58aa18e1fe14 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization commit 7343be2d3b1b8cb1ba0c4c55767b60dbce8f8b22
artbio
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108 "--Rtsne_exaggeration_factor",
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artbio
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109 default = 12.0,
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artbio
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110 type = "numeric",
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artbio
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111 help = " Exaggeration factor used to multiply the P matrix in the first part of the optimization [default : '%default' ]"
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artbio
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112 ),
58aa18e1fe14 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization commit 7343be2d3b1b8cb1ba0c4c55767b60dbce8f8b22
artbio
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113 make_option(
58aa18e1fe14 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization commit 7343be2d3b1b8cb1ba0c4c55767b60dbce8f8b22
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114 "--PCA_npc",
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artbio
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115 default = 5,
58aa18e1fe14 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization commit 7343be2d3b1b8cb1ba0c4c55767b60dbce8f8b22
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116 type = "integer",
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artbio
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117 help = "number of dimensions kept in the results [default : '%default' ]"
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artbio
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118 ),
58aa18e1fe14 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization commit 7343be2d3b1b8cb1ba0c4c55767b60dbce8f8b22
artbio
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119 make_option(
58aa18e1fe14 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization commit 7343be2d3b1b8cb1ba0c4c55767b60dbce8f8b22
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120 "--item_size",
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artbio
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121 default = 1,
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artbio
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122 type = "numeric",
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artbio
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123 help = "Size of points/labels in PCA [default : '%default' ]"
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artbio
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124 ),
58aa18e1fe14 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization commit 7343be2d3b1b8cb1ba0c4c55767b60dbce8f8b22
artbio
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125 make_option(
58aa18e1fe14 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization commit 7343be2d3b1b8cb1ba0c4c55767b60dbce8f8b22
artbio
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126 "--x_axis",
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artbio
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127 default = 1,
58aa18e1fe14 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization commit 7343be2d3b1b8cb1ba0c4c55767b60dbce8f8b22
artbio
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128 type = "integer",
58aa18e1fe14 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization commit 7343be2d3b1b8cb1ba0c4c55767b60dbce8f8b22
artbio
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129 help = "PC to plot in the x axis [default : '%default' ]"
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artbio
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130 ),
58aa18e1fe14 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization commit 7343be2d3b1b8cb1ba0c4c55767b60dbce8f8b22
artbio
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131 make_option(
58aa18e1fe14 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization commit 7343be2d3b1b8cb1ba0c4c55767b60dbce8f8b22
artbio
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132 "--y_axis",
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artbio
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133 default = 2,
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artbio
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134 type = "integer",
58aa18e1fe14 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization commit 7343be2d3b1b8cb1ba0c4c55767b60dbce8f8b22
artbio
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135 help = "PC to plot in the y axis [default : '%default' ]"
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artbio
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diff changeset
136 ),
58aa18e1fe14 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization commit 7343be2d3b1b8cb1ba0c4c55767b60dbce8f8b22
artbio
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137 make_option(
58aa18e1fe14 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization commit 7343be2d3b1b8cb1ba0c4c55767b60dbce8f8b22
artbio
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138 "--HCPC_ncluster",
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artbio
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139 default = -1,
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artbio
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140 type = "numeric",
58aa18e1fe14 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization commit 7343be2d3b1b8cb1ba0c4c55767b60dbce8f8b22
artbio
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141 help = "nb.clust, number of clusters to consider in the hierarchical clustering. [default : -1 let HCPC to optimize the number]"
58aa18e1fe14 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization commit 7343be2d3b1b8cb1ba0c4c55767b60dbce8f8b22
artbio
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diff changeset
142 ),
58aa18e1fe14 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization commit 7343be2d3b1b8cb1ba0c4c55767b60dbce8f8b22
artbio
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143 make_option(
58aa18e1fe14 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization commit 7343be2d3b1b8cb1ba0c4c55767b60dbce8f8b22
artbio
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144 "--HCPC_npc",
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artbio
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145 default = 5,
58aa18e1fe14 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization commit 7343be2d3b1b8cb1ba0c4c55767b60dbce8f8b22
artbio
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146 type = "integer",
58aa18e1fe14 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization commit 7343be2d3b1b8cb1ba0c4c55767b60dbce8f8b22
artbio
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147 help = "npc, number of dimensions which are kept for HCPC analysis [default : '%default' ]"
58aa18e1fe14 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization commit 7343be2d3b1b8cb1ba0c4c55767b60dbce8f8b22
artbio
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diff changeset
148 ),
58aa18e1fe14 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization commit 7343be2d3b1b8cb1ba0c4c55767b60dbce8f8b22
artbio
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149 make_option(
58aa18e1fe14 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization commit 7343be2d3b1b8cb1ba0c4c55767b60dbce8f8b22
artbio
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150 "--HCPC_metric",
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artbio
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151 default = "euclidean",
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artbio
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diff changeset
152 type = "character",
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artbio
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153 help = "Metric to be used for calculating dissimilarities between observations, available 'euclidean' or 'manhattan' [default : '%default' ]"
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artbio
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154 ),
58aa18e1fe14 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization commit 7343be2d3b1b8cb1ba0c4c55767b60dbce8f8b22
artbio
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diff changeset
155 make_option(
58aa18e1fe14 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization commit 7343be2d3b1b8cb1ba0c4c55767b60dbce8f8b22
artbio
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156 "--HCPC_method",
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artbio
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157 default = "ward",
58aa18e1fe14 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization commit 7343be2d3b1b8cb1ba0c4c55767b60dbce8f8b22
artbio
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diff changeset
158 type = "character",
58aa18e1fe14 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization commit 7343be2d3b1b8cb1ba0c4c55767b60dbce8f8b22
artbio
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159 help = "Clustering method between 'ward','average','single', 'complete', 'weighted' [default :'%default']"
58aa18e1fe14 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization commit 7343be2d3b1b8cb1ba0c4c55767b60dbce8f8b22
artbio
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160 ),
58aa18e1fe14 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization commit 7343be2d3b1b8cb1ba0c4c55767b60dbce8f8b22
artbio
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diff changeset
161 make_option(
58aa18e1fe14 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization commit 7343be2d3b1b8cb1ba0c4c55767b60dbce8f8b22
artbio
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162 "--pdf_out",
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artbio
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163 default = "out.pdf",
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artbio
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164 type = "character",
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artbio
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165 help = "pdf of plots [default : '%default' ]"
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artbio
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166 ),
58aa18e1fe14 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization commit 7343be2d3b1b8cb1ba0c4c55767b60dbce8f8b22
artbio
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diff changeset
167 make_option(
58aa18e1fe14 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization commit 7343be2d3b1b8cb1ba0c4c55767b60dbce8f8b22
artbio
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168 "--HCPC_consol",
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artbio
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169 default = "TRUE",
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170 type = "logical",
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171 help = "If TRUE, a k-means consolidation is performed [default :'%default']"
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172 ),
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173 make_option(
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174 "--HCPC_itermax",
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175 default = "10",
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176 type = "integer",
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177 help = "The maximum number of iterations for the consolidation [default :'%default']"
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178 ),
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179 make_option(
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180 "--HCPC_min",
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181 default = "3",
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182 type = "integer",
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183 help = "The least possible number of clusters suggested [default :'%default']"
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184 ),
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185 make_option(
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186 "--HCPC_max",
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187 default = -1,
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188 type = "integer",
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189 help = "The higher possible number of clusters suggested [default :'%default']"
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190 ),
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191 make_option(
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192 "--HCPC_clusterCA",
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193 default = "rows",
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194 type = "character",
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195 help = "A string equals to 'rows' or 'columns' for the clustering of Correspondence Analysis results [default :'%default']"
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196 ),
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197 make_option(
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198 "--HCPC_kk",
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199 default = Inf,
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200 type = "numeric",
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201 help = "The maximum number of iterations for the consolidation [default :'%default']"
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202 ),
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203 make_option(
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204 "--HCPC_mutual_info",
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205 default = "",
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206 type = "character",
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207 help = "Output file of external validation of HCPC clustering with factor levels [default :'%default']"
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208 ),
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209 make_option(
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210 "--HCPC_cell_clust",
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211 default = "",
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212 type = "character",
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213 help = "Lists cells in the clusters generated by HCPC clustering. 2-column table (cell identifiers/clusters) [default :'%default']"
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214 ),
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215 make_option(
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216 "--HCPC_contributions",
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217 default = "",
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218 type = "character",
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219 help = "Table of variables (genes) most contributing to HCPC clustering [default :'%default']"
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220 )
0
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221 )
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222
7
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223 opt <- parse_args(OptionParser(option_list = option_list),
9
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224 args = commandArgs(trailingOnly = TRUE)
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225 )
0
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226
7
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227 if (opt$HCPC_max == -1) {
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228 opt$HCPC_max <- NULL
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229 }
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230 if (opt$HCPC_kk == -1) {
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231 opt$HCPC_kk <- Inf
7
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232 }
0
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233
8
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234 #### We treat data once, at the beginning of the script ####
7
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235 data <- read.delim(
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236 opt$data,
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237 check.names = FALSE,
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238 header = TRUE,
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239 row.names = 1,
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240 sep = "\t"
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241 )
8
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242 # we transpose immediately, because this is the common data structure
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243 data <- as.data.frame(t(data))
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244
8
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245 # we treat the factor for usage in 3 methods
7
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246 if (opt$factor != "") {
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247 contrasting_factor <- read.delim(opt$factor, header = TRUE)
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248 rownames(contrasting_factor) <- contrasting_factor[, 1]
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249 # we pick only the relevant values of the contrasting factor
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250 contrasting_factor <- contrasting_factor[rownames(data), ]
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251 sup <- colnames(contrasting_factor)[2]
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252 if (!is.numeric(contrasting_factor[, 2])) {
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253 contrasting_factor[, 2] <- as.factor(contrasting_factor[, 2])
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254 }
8
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255 }
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256
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257 ######### make PCA with FactoMineR #################
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258 if (opt$visu_choice == "PCA") {
9
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259 if (opt$labels) {
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260 labels <- "ind"
4
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261 } else {
9
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262 labels <- "none"
4
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263 }
9
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264 pdf(opt$pdf_out)
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265 if (opt$factor != "") {
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266 data <- cbind(data, contrasting_factor[, 2])
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267 colnames(data)[length(data)] <- sup
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268 if (is.numeric(contrasting_factor[, 2])) {
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269 res_pca <- PCA(X = data, quanti.sup = sup, graph = FALSE)
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270 pca_plot <- plot(res_pca,
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271 habillage = sup, label = labels,
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272 title = "PCA graph of cells", cex = opt$item_size,
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273 axes = c(opt$x_axis, opt$y_axis)
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274 )
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275 } else {
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276 res_pca <- PCA(X = data, quali.sup = sup, graph = FALSE)
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277 pca_plot <- plot(res_pca,
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278 habillage = sup, label = labels,
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279 title = "PCA graph of cells", cex = opt$item_size,
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280 axes = c(opt$x_axis, opt$y_axis)
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281 )
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282 }
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283 } else {
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284 res_pca <- PCA(X = data, graph = FALSE)
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285 pca_plot <- plot(res_pca,
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286 label = labels,
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287 title = "PCA graph of cells", cex = opt$item_size,
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288 axes = c(opt$x_axis, opt$y_axis), col.ind = "deepskyblue4"
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289 )
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290 }
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291 print(pca_plot)
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292 dev.off()
0
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293 }
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294
8
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295 ########### make HCPC with FactoMineR ##########
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296 if (opt$visu_choice == "HCPC") {
9
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297 pdf(opt$pdf_out)
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298 # HCPC starts with a PCA
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299 pca <- PCA(X = data, ncp = opt$HCPC_npc, graph = FALSE)
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300 pca_ind_coord <- as.data.frame(pca$ind$coord) # coordinates of observations in PCA
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301 # Hierarchical Clustering On Principal Components Followed By Kmean Clustering
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302 res_hcpc <- HCPC(pca,
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303 nb.clust = opt$HCPC_ncluster,
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304 metric = opt$HCPC_metric,
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305 method = opt$HCPC_method,
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306 graph = FALSE,
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307 consol = opt$HCPC_consol,
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308 iter.max = opt$HCPC_itermax,
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309 min = opt$HCPC_min,
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310 max = opt$HCPC_max,
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311 cluster.CA = opt$HCPC_clusterCA,
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312 kk = opt$HCPC_kk
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313 )
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314 # HCPC plots
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315 dims <- head(as.data.frame(res_hcpc$call$t$res$eig), 2) # dims variances in column 2
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316 plot(res_hcpc, choice = "tree")
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317 plot(res_hcpc, choice = "bar")
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318 if (opt$labels == FALSE) {
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319 plot(res_hcpc, choice = "3D.map", ind.names = FALSE)
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320 plot(res_hcpc, choice = "map", label = "none")
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321 } else {
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322 plot(res_hcpc, choice = "3D.map")
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323 plot(res_hcpc, choice = "map")
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324 }
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325 ## Normalized Mutual Information
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326 if (opt$factor != "") {
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327 sink(opt$HCPC_mutual_info)
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328 cat("Relationship between input factor and its levels and the HCPC clusters")
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329 res <- external_validation(
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330 true_labels = as.numeric(contrasting_factor[, 2]),
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331 clusters = as.numeric(res_hcpc$data.clust$clust),
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332 summary_stats = TRUE
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333 )
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334 sink()
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335 }
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336 dev.off()
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337
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338 res_clustering <- data.frame(
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339 Cell = rownames(res_hcpc$data.clust),
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340 Cluster = res_hcpc$data.clust$clust
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341 )
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342 # Description of cluster by most contributing variables / gene expressions
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343 # first transform list of vectors in a list of dataframes
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344 extract_description <- lapply(res_hcpc$desc.var$quanti, as.data.frame)
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345 # second, transfer rownames (genes) to column in the dataframe, before rbinding
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346 extract_description_w_genes <- Map(cbind,
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347 extract_description,
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348 genes = lapply(extract_description, rownames)
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349 )
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350 # Then collapse all dataframes with cluster_id in 1st column using {data.table} rbindlist()
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351 cluster_description <- rbindlist(extract_description_w_genes, idcol = "cluster_id")
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352 cluster_description <- cluster_description[, c(8, 1, 2, 3, 4, 5, 6, 7)] # swap columns
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353 cluster_description <- cluster_description[order(
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354 cluster_description[[2]],
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355 cluster_description[[8]]
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356 ), ] # sort by cluster then by pval
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357 # Finally, output cluster description data frame
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358 write.table(cluster_description,
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359 file = opt$HCPC_contributions,
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360 sep = "\t",
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361 quote = FALSE,
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362 col.names = TRUE,
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363 row.names = FALSE
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364 )
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365
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366 ## Return cluster table to user
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367 write.table(res_clustering,
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368 file = opt$HCPC_cell_clust,
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369 sep = "\t",
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370 quote = FALSE,
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371 col.names = TRUE,
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372 row.names = FALSE
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373 )
8
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374 }
0
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375 ################ t-SNE ####################
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376 if (opt$visu_choice == "tSNE") {
9
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377 set.seed(opt$Rtsne_seed) ## Sets seed for reproducibility
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378 tsne_out <- Rtsne(data,
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379 dims = opt$Rtsne_dims,
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380 initial_dims = opt$Rtsne_initial_dims,
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381 perplexity = opt$Rtsne_perplexity,
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382 theta = opt$Rtsne_theta,
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383 max_iter = opt$Rtsne_max_iter,
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384 pca = opt$Rtsne_pca,
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385 pca_center = opt$Rtsne_pca_center,
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386 pca_scale = opt$Rtsne_pca_scale,
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387 normalize = opt$Rtsne_normalize,
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388 exaggeration_factor = opt$Rtsne_exaggeration_factor
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389 )
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390 embedding <- as.data.frame(tsne_out$Y[, 1:2])
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391 embedding$Class <- as.factor(rownames(data))
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392 gg_legend <- theme(legend.position = "right")
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393 pointcolor <- "#E70000"
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394 pointsize <- opt$item_size * 1.5
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395 the_theme <- theme(
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396 panel.background = element_rect(
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397 fill = "gray100", colour = "#6D9EC1",
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398 size = 2, linetype = "solid"
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399 ),
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400 panel.grid.major = element_line(
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401 size = 0.5, linetype = "solid",
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402 colour = "#6D9EC1"
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403 ),
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404 panel.grid.minor = element_line(
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405 size = 0.25, linetype = "solid",
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406 colour = "darkslategray3"
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407 )
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408 )
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409 if (opt$factor == "") {
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410 p <- ggplot(embedding, aes(x = V1, y = V2)) +
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411 geom_point(size = pointsize * 0.25, color = pointcolor) +
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412 gg_legend +
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413 xlab("t-SNE 1") +
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414 ylab("t-SNE 2") +
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415 ggtitle("t-SNE") +
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416 the_theme +
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417 if (opt$labels) {
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418 geom_text(aes(label = Class), hjust = -0.2, vjust = -0.5, size = pointsize, color = pointcolor)
58aa18e1fe14 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization commit 7343be2d3b1b8cb1ba0c4c55767b60dbce8f8b22
artbio
parents: 8
diff changeset
419 }
8
fe6f76030168 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization commit a3dc683410fc240f428c8fbee3c63aa9965fbf38
artbio
parents: 7
diff changeset
420 } else {
9
58aa18e1fe14 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization commit 7343be2d3b1b8cb1ba0c4c55767b60dbce8f8b22
artbio
parents: 8
diff changeset
421 if (is.numeric(contrasting_factor[, 2])) {
58aa18e1fe14 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization commit 7343be2d3b1b8cb1ba0c4c55767b60dbce8f8b22
artbio
parents: 8
diff changeset
422 embedding$factor <- contrasting_factor[, 2]
58aa18e1fe14 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization commit 7343be2d3b1b8cb1ba0c4c55767b60dbce8f8b22
artbio
parents: 8
diff changeset
423 } else {
58aa18e1fe14 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization commit 7343be2d3b1b8cb1ba0c4c55767b60dbce8f8b22
artbio
parents: 8
diff changeset
424 embedding$factor <- as.factor(contrasting_factor[, 2])
58aa18e1fe14 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization commit 7343be2d3b1b8cb1ba0c4c55767b60dbce8f8b22
artbio
parents: 8
diff changeset
425 }
58aa18e1fe14 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization commit 7343be2d3b1b8cb1ba0c4c55767b60dbce8f8b22
artbio
parents: 8
diff changeset
426 p <- ggplot(embedding, aes(x = V1, y = V2, color = factor)) +
58aa18e1fe14 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization commit 7343be2d3b1b8cb1ba0c4c55767b60dbce8f8b22
artbio
parents: 8
diff changeset
427 geom_point(size = pointsize * 0.25) +
58aa18e1fe14 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization commit 7343be2d3b1b8cb1ba0c4c55767b60dbce8f8b22
artbio
parents: 8
diff changeset
428 gg_legend +
58aa18e1fe14 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization commit 7343be2d3b1b8cb1ba0c4c55767b60dbce8f8b22
artbio
parents: 8
diff changeset
429 xlab("t-SNE 1") +
58aa18e1fe14 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization commit 7343be2d3b1b8cb1ba0c4c55767b60dbce8f8b22
artbio
parents: 8
diff changeset
430 ylab("t-SNE 2") +
58aa18e1fe14 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization commit 7343be2d3b1b8cb1ba0c4c55767b60dbce8f8b22
artbio
parents: 8
diff changeset
431 ggtitle("t-SNE") +
58aa18e1fe14 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization commit 7343be2d3b1b8cb1ba0c4c55767b60dbce8f8b22
artbio
parents: 8
diff changeset
432 the_theme +
58aa18e1fe14 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization commit 7343be2d3b1b8cb1ba0c4c55767b60dbce8f8b22
artbio
parents: 8
diff changeset
433 if (opt$labels) {
58aa18e1fe14 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization commit 7343be2d3b1b8cb1ba0c4c55767b60dbce8f8b22
artbio
parents: 8
diff changeset
434 geom_text(aes(label = Class, colour = factor), hjust = -0.2, vjust = -0.5, size = pointsize)
58aa18e1fe14 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization commit 7343be2d3b1b8cb1ba0c4c55767b60dbce8f8b22
artbio
parents: 8
diff changeset
435 }
7
18a1dc4aec4a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit ef87a68f9a33f8418699d97627eb5f49a5e2c4a6
artbio
parents: 6
diff changeset
436 }
9
58aa18e1fe14 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization commit 7343be2d3b1b8cb1ba0c4c55767b60dbce8f8b22
artbio
parents: 8
diff changeset
437 pdf(opt$pdf_out)
58aa18e1fe14 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization commit 7343be2d3b1b8cb1ba0c4c55767b60dbce8f8b22
artbio
parents: 8
diff changeset
438 print(p)
58aa18e1fe14 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization commit 7343be2d3b1b8cb1ba0c4c55767b60dbce8f8b22
artbio
parents: 8
diff changeset
439 dev.off()
0
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
440 }