Mercurial > repos > artbio > gsc_high_dimensions_visualisation
annotate high_dim_visu.R @ 0:cad0001b9cfb draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
author | artbio |
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date | Mon, 24 Jun 2019 13:39:11 -0400 |
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children | 7e7a2a4cfce2 |
rev | line source |
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0
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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1 # load packages that are provided in the conda env |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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2 options( show.error.messages=F, |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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3 error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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4 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
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5 requiredPackages = c('optparse', 'Rtsne', 'ggplot2', 'ggfortify') |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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6 warnings() |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
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7 library(optparse) |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
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8 library(FactoMineR) |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
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9 library(factoextra) |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
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10 library(Rtsne) |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
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11 library(ggplot2) |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
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12 library(ggfortify) |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
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13 library(RColorBrewer) |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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14 |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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15 |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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16 # Arguments |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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17 option_list = list( |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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18 make_option( |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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19 "--data", |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
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20 default = NA, |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
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21 type = 'character', |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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22 help = "Input file that contains expression value to visualise" |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
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23 ), |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
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24 make_option( |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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25 "--sep", |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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26 default = '\t', |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
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27 type = 'character', |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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28 help = "File separator [default : '%default' ]" |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
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29 ), |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
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30 make_option( |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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31 "--colnames", |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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32 default = TRUE, |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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33 type = 'logical', |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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34 help = "Consider first line as header ? [default : '%default' ]" |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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35 ), |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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36 make_option( |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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37 "--out", |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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38 default = "res.tab", |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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39 type = 'character', |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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40 help = "Output name [default : '%default' ]" |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
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41 ), |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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42 make_option( |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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43 "--labels", |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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44 default = FALSE, |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
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45 type = 'logical', |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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46 help = "add labels in scatter plots [default : '%default' ]" |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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47 ), |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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48 make_option( |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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49 "--factor", |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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50 default = '', |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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51 type = 'character', |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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52 help = "A two column table that specifies factor levels for contrasting data [default : '%default' ]" |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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53 ), |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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54 make_option( |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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55 "--visu_choice", |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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56 default = 'PCA', |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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57 type = 'character', |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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58 help = "visualisation method ('PCA', 'tSNE', 'HCPC') [default : '%default' ]" |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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59 ), |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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60 make_option( |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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61 "--table_coordinates", |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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62 default = '', |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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63 type = 'character', |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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64 help = "Table with plot coordinates [default : '%default' ]" |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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65 ), |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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66 make_option( |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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67 "--Rtsne_seed", |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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68 default = 42, |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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69 type = 'integer', |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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70 help = "Seed value for reproducibility [default : '%default' ]" |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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71 ), |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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72 make_option( |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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73 "--Rtsne_dims", |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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74 default = 2, |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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75 type = 'integer', |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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76 help = "Output dimensionality [default : '%default' ]" |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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77 ), |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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78 make_option( |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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79 "--Rtsne_initial_dims", |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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80 default = 50, |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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81 type = 'integer', |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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82 help = "The number of dimensions that should be retained in the initial PCA step [default : '%default' ]" |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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83 ), |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
84 make_option( |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
85 "--Rtsne_perplexity", |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
86 default = 5.0, |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
87 type = 'numeric', |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
88 help = "perplexity [default : '%default' ]" |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
89 ), |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
90 make_option( |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
91 "--Rtsne_theta", |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
92 default = 1.0, |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
93 type = 'numeric', |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
94 help = "theta [default : '%default' ]" |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
95 ), |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
96 make_option( |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
97 "--Rtsne_max_iter", |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
98 default = 1000, |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
99 type = 'integer', |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
100 help = "max_iter [default : '%default' ]" |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
101 ), |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
102 make_option( |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
103 "--Rtsne_pca", |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
104 default = TRUE, |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
105 type = 'logical', |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
106 help = "Whether an initial PCA step should be performed [default : '%default' ]" |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
107 ), |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
108 make_option( |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
109 "--Rtsne_pca_center", |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
110 default = TRUE, |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
111 type = 'logical', |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
112 help = "Should data be centered before pca is applied? [default : '%default' ]" |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
113 ), |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
114 make_option( |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
115 "--Rtsne_pca_scale", |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
116 default = FALSE, |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
117 type = 'logical', |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
118 help = "Should data be scaled before pca is applied? [default : '%default' ]" |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
119 ), |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
120 make_option( |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
121 "--Rtsne_normalize", |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
122 default = TRUE, |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
123 type = 'logical', |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
124 help = "Should data be normalized internally prior to distance calculations? [default : '%default' ]" |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
125 ), |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
126 make_option( |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
127 "--Rtsne_exaggeration_factor", |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
128 default = 12.0, |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
129 type = 'numeric', |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
130 help = " Exaggeration factor used to multiply the P matrix in the first part of the optimization [default : '%default' ]" |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
131 ), |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
132 make_option( |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
133 "--PCA_npc", |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
134 default = 5, |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
135 type = 'integer', |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
136 help = "number of dimensions kept in the results [default : '%default' ]" |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
137 ), |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
138 make_option( |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
139 "--HCPC_ncluster", |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
140 default = -1, |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
141 type = 'numeric', |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
142 help = "nb.clust, number of clusters to consider in the hierarchical clustering. [default : -1 let HCPC to optimize the number]" |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
143 ), |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
144 make_option( |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
145 "--HCPC_npc", |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
146 default = 5, |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
147 type = 'integer', |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
148 help = "npc, number of dimensions which are kept for HCPC analysis [default : '%default' ]" |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
149 ), |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
150 make_option( |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
151 "--HCPC_metric", |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
152 default = 'euclidian', |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
153 type = 'character', |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
154 help = "Metric to be used for calculating dissimilarities between observations, available 'euclidian' or 'manhattan' [default : '%default' ]" |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
155 ), |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
156 make_option( |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
157 "--HCPC_method", |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
158 default = 'ward', |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
159 type = 'character', |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
160 help = "Clustering method between 'ward','average','single', 'complete', 'weighted' [default :'%default']" |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
161 ), |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
162 make_option( |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
163 "--pdf_out", |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
164 default = "out.pdf", |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
165 type = 'character', |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
166 help = "pdf of plots [default : '%default' ]" |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
167 ), |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
168 make_option( |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
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169 "--HCPC_consol", |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
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170 default = 'TRUE', |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
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171 type = 'logical', |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
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172 help = "If TRUE, a k-means consolidation is performed [default :'%default']" |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
173 ), |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
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174 make_option( |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
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175 "--HCPC_itermax", |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
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176 default = '10', |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
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177 type = 'integer', |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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178 help = "The maximum number of iterations for the consolidation [default :'%default']" |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
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179 ), |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
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180 make_option( |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
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181 "--HCPC_min", |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
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182 default = '3', |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
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183 type = 'integer', |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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184 help = "The least possible number of clusters suggested [default :'%default']" |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
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185 ), |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
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186 make_option( |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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187 "--HCPC_max", |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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188 default = -1, |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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189 type = 'integer', |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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190 help = "The higher possible number of clusters suggested [default :'%default']" |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
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191 ), |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
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192 make_option( |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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193 "--HCPC_clusterCA", |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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194 default = 'rows', |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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195 type = 'character', |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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196 help = "A string equals to 'rows' or 'columns' for the clustering of Correspondence Analysis results [default :'%default']" |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
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197 ), |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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198 make_option( |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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199 "--HCPC_kk", |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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200 default = -1, |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
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201 type = 'numeric', |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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202 help = "The maximum number of iterations for the consolidation [default :'%default']" |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
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|
203 ) |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
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|
204 ) |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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205 |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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206 opt = parse_args(OptionParser(option_list = option_list), |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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207 args = commandArgs(trailingOnly = TRUE)) |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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208 |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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209 if (opt$sep == "tab") {opt$sep <- "\t"} |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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210 if (opt$sep == "comma") {opt$sep <- ","} |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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211 if(opt$HCPC_max == -1) {opt$HCPC_max <- NULL} |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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212 if(opt$HCPC_kk == -1) {opt$HCPC_kk <- Inf} |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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213 |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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214 data = read.table( |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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215 opt$data, |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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216 check.names = FALSE, |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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217 header = opt$colnames, |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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218 row.names = 1, |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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219 sep = opt$sep |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
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|
220 ) |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
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221 |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
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222 # Contrasting factor and its colors |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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223 if (opt$factor != '') { |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
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224 contrasting_factor <- read.delim( |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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225 opt$factor, |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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226 header = TRUE |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
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|
227 ) |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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228 rownames(contrasting_factor) <- contrasting_factor[,1] |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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229 contrasting_factor <- contrasting_factor[colnames(data),] |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
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230 colnames(contrasting_factor) <- c("id","factor") |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
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231 contrasting_factor$factor <- as.factor(contrasting_factor$factor) |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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232 factorColors <- |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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233 with(contrasting_factor, |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
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|
234 data.frame(factor = levels(factor), |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
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|
235 data.frame(factor = levels(factor), |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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236 color = I(brewer.pal(nlevels(factor), name = 'Paired')))) |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
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|
237 ) |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
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|
238 factor_cols <- factorColors$color[match(contrasting_factor$factor, |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
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|
239 factorColors$factor)] |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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240 } else { |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
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241 factor_cols <- rep("deepskyblue4", length(rownames(data))) |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
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|
242 } |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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|
243 |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
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|
244 ################ t-SNE #################### |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
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|
245 if (opt$visu_choice == 'tSNE') { |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
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|
246 # filter and transpose df for tsne and pca |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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|
247 tdf = t(data) |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
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248 # make tsne and plot results |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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249 set.seed(opt$Rtsne_seed) ## Sets seed for reproducibility |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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250 |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
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251 tsne_out <- Rtsne(tdf, |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
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252 dims = opt$Rtsne_dims, |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
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253 initial_dims = opt$Rtsne_initial_dims, |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
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254 perplexity = opt$Rtsne_perplexity , |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
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255 theta = opt$Rtsne_theta, |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
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256 max_iter = opt$Rtsne_max_iter, |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
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257 pca = opt$Rtsne_pca, |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
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258 pca_center = opt$Rtsne_pca_center, |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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259 pca_scale = opt$Rtsne_pca_scale, |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
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260 normalize = opt$Rtsne_normalize, |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
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261 exaggeration_factor=opt$Rtsne_exaggeration_factor) |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
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262 |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
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263 embedding <- as.data.frame(tsne_out$Y[,1:2]) |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
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264 embedding$Class <- as.factor(rownames(tdf)) |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
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265 gg_legend = theme(legend.position="right") |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
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266 if (opt$factor == '') { |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
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267 ggplot(embedding, aes(x=V1, y=V2)) + |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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268 geom_point(size=1, color='deepskyblue4') + |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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269 gg_legend + |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
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270 xlab("") + |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
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271 ylab("") + |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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272 ggtitle('t-SNE') + |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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273 if (opt$labels) { |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
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274 geom_text(aes(label=Class),hjust=-0.2, vjust=-0.5, size=1.5, color='deepskyblue4') |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
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275 } |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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276 } else { |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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277 embedding$factor <- as.factor(contrasting_factor$factor) |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
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278 ggplot(embedding, aes(x=V1, y=V2, color=factor)) + |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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279 geom_point(size=1) + #, color=factor_cols |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
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280 gg_legend + |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
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281 xlab("") + |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
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282 ylab("") + |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
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283 ggtitle('t-SNE') + |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
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284 if (opt$labels) { |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
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285 geom_text(aes(label=Class, colour=factor),hjust=-0.2, vjust=-0.5, size=1.5) |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
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286 } |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
287 } |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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288 ggsave(file=opt$pdf_out, device="pdf") |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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289 |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
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290 #save coordinates table |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
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291 if(opt$table_coordinates != ''){ |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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292 coord_table <- cbind(rownames(tdf),as.data.frame(tsne_out$Y)) |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
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293 colnames(coord_table)=c("Cells",paste0("DIM",(1:opt$Rtsne_dims))) |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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diff
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|
294 } |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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295 } |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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296 |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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297 |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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298 ######### make PCA with FactoMineR ################# |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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299 if (opt$visu_choice == 'PCA') { |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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300 pca <- PCA(t(data), ncp=opt$PCA_npc, graph=FALSE) |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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301 pdf(opt$pdf_out) |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
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302 if (opt$labels == FALSE) { |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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303 plot(pca, label="none" , col.ind = factor_cols) |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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304 } else { |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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305 plot(pca, cex=0.2 , col.ind = factor_cols) |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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306 } |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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307 if (opt$factor != '') { |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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308 legend(x = 'topright', |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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309 legend = as.character(factorColors$factor), |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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310 col = factorColors$color, pch = 16, bty = 'n', xjust = 1, cex=0.7) |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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311 } |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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312 dev.off() |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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313 |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
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314 #save coordinates table |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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315 if(opt$table_coordinates != ''){ |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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316 coord_table <- cbind(rownames(pca$ind$coord),as.data.frame(pca$ind$coord)) |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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317 colnames(coord_table)=c("Cells",paste0("DIM",(1:opt$PCA_npc))) |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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318 } |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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319 |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
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|
320 } |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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321 |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
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|
322 ########### make HCPC with FactoMineR ########## |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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323 if (opt$visu_choice == 'HCPC') { |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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324 |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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325 # HCPC starts with a PCA |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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326 pca <- PCA( |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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327 t(data), |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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328 ncp = opt$HCPC_npc, |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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329 graph = FALSE, |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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330 scale.unit = FALSE |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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331 ) |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
332 |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
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333 PCA_IndCoord = as.data.frame(pca$ind$coord) # coordinates of observations in PCA |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
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334 |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
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335 # Hierarchical Clustering On Principal Components Followed By Kmean Clustering |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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336 res.hcpc <- HCPC(pca, |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
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337 nb.clust=opt$HCPC_ncluster, metric=opt$HCPC_metric, method=opt$HCPC_method, |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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338 graph=F,consol=opt$HCPC_consol,iter.max=opt$HCPC_itermax,min=opt$HCPC_min,max=opt$HCPC_max, |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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339 cluster.CA=opt$HCPC_clusterCA,kk=opt$HCPC_kk) |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
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340 # HCPC plots |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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341 dims <- head(as.data.frame(res.hcpc$call$t$res$eig),2) # dims variances in column 2 |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
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342 pdf(opt$pdf_out) |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
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343 plot(res.hcpc, choice="tree") |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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344 plot(res.hcpc, choice="bar") |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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345 plot(res.hcpc, choice="3D.map") |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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346 if (opt$labels == FALSE) { |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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347 plot(res.hcpc, choice="map", label="none") |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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348 } else { |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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349 plot(res.hcpc, choice="map") |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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|
350 } |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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351 |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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352 # user contrasts on the pca |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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353 if (opt$factor != '') { |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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354 plot(pca, label="none", habillage="ind", col.hab=factor_cols) |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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changeset
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355 legend(x = 'topright', |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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356 legend = as.character(factorColors$factor), |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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357 col = factorColors$color, pch = 16, bty = 'n', xjust = 1, cex=0.7) |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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358 } |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
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359 ## Clusters to which individual observations belong # used ? |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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360 # Clust <- data.frame(Cluster = res.hcpc$data.clust[, (nrow(data) + 1)], |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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361 # Observation = rownames(res.hcpc$data.clust)) |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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362 # metadata <- data.frame(Observation=colnames(data), row.names=colnames(data)) |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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363 # metadata = merge(y = metadata, |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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364 # x = Clust, |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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365 # by = "Observation") |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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366 |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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367 # unclear utility |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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368 # ObsNumberPerCluster = as.data.frame(table(metadata$Cluster)) |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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369 # colnames(ObsNumberPerCluster) = c("Cluster", "ObsNumber") |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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|
370 # |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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371 # ## Silhouette Plot # not used |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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372 # hc.cut = hcut(PCA_IndCoord, |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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373 # k = nlevels(metadata$Cluster), |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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374 # hc_method = "ward.D2") |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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375 # |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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376 # Sil = fviz_silhouette(hc.cut) |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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377 # sil1 = as.data.frame(Sil$data) |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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|
378 |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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379 ## Normalized Mutual Information # to be implemented later |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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380 # sink(opt$mutual_info) |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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381 # res = external_validation( |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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382 # as.numeric(factor(metadata[, Patient])), |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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383 # as.numeric(metadata$Cluster), |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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384 # method = "adjusted_rand_index", |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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385 # summary_stats = TRUE |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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386 # ) |
cad0001b9cfb
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artbio
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387 # sink() |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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388 dev.off() |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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389 |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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390 if(opt$table_coordinates != ''){ |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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391 coord_table <- cbind(Cell=rownames(res.hcpc$call$X),as.data.frame(res.hcpc$call$X)) |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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392 colnames(coord_table)=c("Cells",paste0("DIM",(1:opt$HCPC_npc)),"Cluster") |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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|
393 } |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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394 } |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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395 |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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396 ## Return coordinates file to user |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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397 |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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398 if(opt$table_coordinates != ''){ |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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399 write.table( |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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400 coord_table, |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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401 file = opt$table_coordinates, |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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402 sep = "\t", |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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403 quote = F, |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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404 col.names = T, |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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405 row.names = F |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
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|
406 ) |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
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|
407 } |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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408 |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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|
409 |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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|
410 |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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changeset
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411 |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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412 |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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413 |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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415 |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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418 |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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419 |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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420 |
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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