Mercurial > repos > dlalgroup > pmids_to_pubtator_matrix

annotate simtext_app.R @ 0:3f4adc85ba5d draft

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"planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
author dlalgroup
date Thu, 24 Sep 2020 02:01:50 +0000
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1 #!/usr/bin/env Rscript
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2 ### SimText App ###
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3 #
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4 # The tool enables the exploration of data generated by text_to_wordmatrix or pmids_to_pubtator_matrix in a locally run ShinyApp. Features are word clouds for each initial search query, dimension reduction and hierarchical clustering of the binary matrix, and a table with words and their frequency among the search queries.
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5 #
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6 # Input:
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7 #
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8 # 1) Input 1:
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9 # Tab-delimited table with
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10 # - column with search queries starting with "ID_", e.g. "ID_gene" if initial search queries were genes
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11 # - column(s) with grouping factor(s) to compare pre-existing categories of the initial search queries with the grouping based on text. The column names should start with "GROUPING_". If the column name is "GROUPING_disorder", "disorder" will be shown as a grouping variable in the app.
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12 # 2) Input 2:
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13 # Output of text_to_wordmatrix or pmids_to_pubtator_matrix, or binary matrix.
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14 #
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15 # optional arguments:
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16 # -h, --help show help message
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17 # -i INPUT, --input INPUT input file name. add path if file is not in working directory
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18 # -m MATRIX, --matrix MATRIX matrix file name. add path if file is not in working directory
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19 # -p PORT, --port PORT specify port, otherwise randomly selected
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20 #
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21 #Output:
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22 #Shiny app with word clouds, dimensionality reduction plot, dendrogram of hierarchical clustering and table with words and their frequency among the entities.
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23 #
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24 #Packages
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25
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26 if ( '--install_packages' %in% commandArgs()) {
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27 print('Installing packages')
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28 if (!require('shiny')) install.packages('shiny', repo="http://cran.rstudio.com/");
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29 if (!require('plotly')) install.packages('plotly', repo="http://cran.rstudio.com/");
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30 if (!require('DT')) install.packages('DT', repo="http://cran.rstudio.com/");
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31 if (!require('shinycssloaders')) install.packages('shinycssloaders', repo="http://cran.rstudio.com/");
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32 if (!require('shinythemes')) install.packages('shinythemes', repo="http://cran.rstudio.com/");
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33 if (!require('tableHTML')) install.packages('tableHTML', repo="http://cran.rstudio.com/");
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34 if (!require('argparse')) install.packages('argparse', repo="http://cran.rstudio.com/");
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35 if (!require('PubMedWordcloud')) install.packages('PubMedWordcloud', repo="http://cran.rstudio.com/");
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36 if (!require('ggplot2')) install.packages('ggplot2', repo="http://cran.rstudio.com/");
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37 if (!require('stringr')) install.packages('stringr', repo="http://cran.rstudio.com/");
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38 if (!require('tidyr')) install.packages('tidyr', repo="http://cran.rstudio.com/");
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39 if (!require('magrittr')) install.packages('magrittr', repo="http://cran.rstudio.com/");
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40 if (!require('plyr')) install.packages('plyr', repo="http://cran.rstudio.com/");
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41 if (!require('ggpubr')) install.packages('ggpubr', repo="http://cran.rstudio.com/");
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42 if (!require('rafalib')) install.packages('rafalib', repo="http://cran.rstudio.com/");
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43 if (!require('RColorBrewer')) install.packages('RColorBrewer', repo="http://cran.rstudio.com/");
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44 if (!require('dendextend')) install.packages('dendextend', repo="http://cran.rstudio.com/");
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45 if (!require('Rtsne')) install.packages('Rtsne', repo="http://cran.rstudio.com/");
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46 if (!require('umap')) install.packages('umap', repo="http://cran.rstudio.com/");
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47 }
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48
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49 suppressPackageStartupMessages(library("shiny"))
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50 suppressPackageStartupMessages(library("plotly"))
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51 suppressPackageStartupMessages(library("DT"))
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52 suppressPackageStartupMessages(library("shinycssloaders"))
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53 suppressPackageStartupMessages(library("shinythemes"))
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54 suppressPackageStartupMessages(library("tableHTML"))
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55 suppressPackageStartupMessages(library("argparse"))
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56 suppressPackageStartupMessages(library("PubMedWordcloud"))
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57 suppressPackageStartupMessages(library("ggplot2"))
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58 suppressPackageStartupMessages(library("stringr"))
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59 suppressPackageStartupMessages(library("tidyr"))
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60 suppressPackageStartupMessages(library("magrittr"))
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61 suppressPackageStartupMessages(library("plyr"))
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62 suppressPackageStartupMessages(library("ggpubr"))
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63 suppressPackageStartupMessages(library("rafalib"))
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64 suppressPackageStartupMessages(library("RColorBrewer"))
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65 suppressPackageStartupMessages(library("dendextend"))
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66 suppressPackageStartupMessages(library("Rtsne"))
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67 suppressPackageStartupMessages(library("umap"))
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68
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69 #command arguments
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70 parser <- ArgumentParser()
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71 parser$add_argument("-i", "--input",
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72 help = "input file name. add path if file is not in working directory")
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73 parser$add_argument("-m", "--matrix", default= NULL,
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74 help = "matrix file name. add path if file is not in working directory")
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75 parser$add_argument("--host", default=NULL,
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76 help="Specify host")
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77 parser$add_argument("-p", "--port", type="integer", default=NULL,
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78 help="Specify port, otherwise randomly select")
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79 parser$add_argument("--install_packages", action="store_true", default=FALSE,
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80 help="If you want to auto install missing required packages.")
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81 args <- parser$parse_args()
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82
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83 # Set host
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84 if(!is.null(args$host)){
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diff changeset
85 options(shiny.host = args$host)
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
86 }
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
87
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
88 # Set port
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
89 if(!is.null(args$port)){
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
90 options(shiny.port = args$port)
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
91 }
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
92
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
93 #load data
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
94 data = read.delim(args$input, stringsAsFactors=FALSE)
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
95 index_grouping = grep("GROUPING_", names(data))
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
96 names(data)[index_grouping] = sub(".*_", "",names(data)[index_grouping])
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
97 colindex_id = grep("^ID_", names(data))
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
98
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
99 matrix = read.delim(args$matrix, check.names = FALSE, header = TRUE, sep='\t')
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
100 matrix = (as.matrix(matrix)>0) *1 #transform matrix to binary matrix
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
101
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
102 ##### UI ######
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
103 ui <- shinyUI(fluidPage(
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
104 navbarPage(theme = shinytheme("flatly"), id = "inTabset",selected = "panel1",
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
105 title = "SimText",
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
106 tabPanel("Home", value = "panel1",
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
107 tabPanel("Results", value = "panel1",
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
108 fluidRow(width=12, offset=0,
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
109 column(width = 4, style = "padding-right: 0px",
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
110 wellPanel(h5(strong("ID of interest")),
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
111 style = "background-color:white;
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
112 border-bottom: 2px solid #EEEEEE;
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
113 border-top-color: white;
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
114 border-right-color: white;
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
115 border-left-color: white;
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
116 box-shadow: 0px 0px 0px white;
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
117 padding:3px;
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
118 width: 100%"),
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
119 selectInput('ID', 'Select ID:', paste0(data[[colindex_id]]," (",seq(1,length(data[[colindex_id]])),")"))),
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
120 column(width = 3, style = "padding-right: 0px",
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
121 wellPanel(h5(strong("Color settings")),
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
122 style = "background-color:white;
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
123 border-bottom: 2px solid #EEEEEE;
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
124 border-top-color: white;
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
125 border-right-color: white;
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
126 border-left-color: white;
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
127 box-shadow: 0px 0px 0px white;
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
128 padding:3px;
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
129 width: 100%"),
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
130 radioButtons('colour', 'Color by:', c("Grouping variable", "Individual word")),
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
131 selectInput("colour_select", "Select:", choices=c(names(data)[index_grouping])))
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
132 ),
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
133 fluidRow(width = 12, offset = 0,
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
134 column(width = 4, #style = "height:650px;",
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
135 wellPanel(textOutput("ID"),
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
136 style = "background-color: #333333;
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
137 color: white;
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
138 border-top-color: #333333;
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
139 border-left-color: #333333;
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
140 border-right-color: #333333;
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
141 box-shadow: 3px 3px 3px #d8d8d8;
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
142 margin-bottom: 0px;
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
143 padding:5px"),
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
144 wellPanel(
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
145 fluidRow(
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
146 column(width = 4,
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
147 numericInput('fontsize', 'Font size:',value = 7, min=1, max=50)),
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
148 column(width = 4,
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
149 numericInput('nword', 'Word number:',value = 50, min=1, max=100)),
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
150 column(width = 12,
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
151 withSpinner(plotOutput("WordcloudPlot",height= "325px"))),
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
152 column(width = 12,
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
153 downloadLink("downloadWordcloud", "Download"))),
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
154 style = "background-color: #ffffff;
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
155 border-bottom-color: #333333;
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
156 border-left-color: #333333;
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
157 height: 470px;
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
158 border-right-color: #333333;
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
159 box-shadow: 3px 3px 3px #d8d8d8;
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
160 margin-top: 0px"),
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
161 wellPanel(textOutput("Table"),
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
162 style = "background-color: #333333;
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
163 color: white;
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
164 border-top-color: #333333;
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
165 border-left-color: #333333;
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
166 border-right-color: #333333;
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
167 box-shadow: 3px 3px 3px #d8d8d8;
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
168 margin-bottom: 0px;
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
169 padding:5px"),
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
170 wellPanel(withSpinner(DT::dataTableOutput("datatable", height= "150px")),
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
171 style = "background-color: #ffffff;
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
172 border-bottom-color: #333333;
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
173 border-left-color: #333333;
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
174 border-right-color: #333333;
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
175 height: 175px;
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
176 box-shadow: 3px 3px 3px #d8d8d8;
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
177 margin-top: 0px")
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
178 ),
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
179 column(width = 8, #style='padding:0px;',
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
180 wellPanel("T-SNE plot of wordmatrix",
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
181 style = "background-color: #333333;
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
182 color: white;
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
183 border-top-color: #333333;
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
184 border-left-color: #333333;
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
185 border-right-color: #333333;
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
186 box-shadow: 3px 3px 3px #d8d8d8;
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
187 margin-bottom: 0px;
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
188 padding:5px"),
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
189 wellPanel(
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
190 fluidRow(
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
191 column(width = 2,
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
192 radioButtons('method', 'Method:',choices=c("t-SNE","UMAP"))),
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
193 column(width = 2,
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
194 numericInput('perplexity', 'Perplexity:',value = 2, min=1, max=nrow(data)-1)),
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
195 column(width = 2,
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
196 radioButtons('label', 'Labels:',choices=c("Index","IDs"))),
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
197 column(width = 2,
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
198 numericInput('labelsize', 'Label size:',value = 12, min=1, max=30)),
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
199 column(width = 8, style='padding:0px;',
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
200 withSpinner(plotlyOutput("TsnePlot",height=550))),
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
201 column(width = 4, style='padding:0px;',
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
202 withSpinner(plotOutput("TsnePlot_legend",height=550))),
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
203 column(width=2,
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
204 downloadLink("downloadPlotdata",label = "Download data"))),
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
205 style = "background-color: white;
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
206 border-bottom-color: #333333;
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
207 border-left-color: #333333;
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
208 border-right-color: #333333;
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
209 box-shadow: 3px 3px 3px #d8d8d8;
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
210 margin-top: 0px"
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
211 #height=575px
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
212 ))),
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
213 fluidRow(column(width = 12,
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
214 wellPanel("Hierarchical clustering of wordmatrix",
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
215 style = "background-color: #333333;
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
216 color: white;
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
217 border-top-color: #333333;
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
218 border-left-color: #333333;
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
219 border-right-color: #333333;
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
220 box-shadow: 3px 3px 3px #d8d8d8;
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
221 margin-bottom: 0px;
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
222 padding:5px")
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
223 ,
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
224 wellPanel(
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
225 fluidRow(
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
226 column(width = 2,
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
227 radioButtons('hcmethod', 'Method:',choices=c("ward.D2","average","complete","single"))),
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
228 column(width = 2,
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
229 numericInput('labelsize_hc', 'Label size:', value = 8, min=1, max=30))
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
230 ),
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
231 fluidRow(
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
232 column(width = 9,
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
233 withSpinner(plotOutput("hclust"))),
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
234 column(width = 3,
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
235 withSpinner(plotOutput("hclust_legend")))
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
236 ),
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
237 style = "background-color: #ffffff;
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
238 border-bottom-color: #333333;
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
239 border-left-color: #333333;
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
240 border-right-color: #333333;
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
241 box-shadow: 3px 3px 3px #d8d8d8;
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
242 margin-top: 0px")
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
243 ,
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
244 verbatimTextOutput("test")
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
245 ))
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
246 ))
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
247
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
248 # ,
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
249 #tabPanel("About", value = "panel2", h3(""))
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
250
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
251 )))
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
252
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
253
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
254
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
255
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
256 ###### SERVER ######
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
257 server <- function(input, output, session) {
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
258
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
259 ##### Global #####
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
260 IDs = reactive(paste0(data[[colindex_id]]," (",seq(1,length(data[[colindex_id]])),")"))
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
261 index_ID = reactive({which(IDs() == input$ID)})
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
262
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
263 ##### Wordcloud plot and download ######
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
264
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
265 output$ID <- renderText({
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
266 paste("Wordcloud of",data[[colindex_id]][index_ID()])
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
267 })
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
268
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
269 output$WordcloudPlot <- renderPlot({
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
270 ID_matrix = matrix[index_ID(),]
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
271 ID_matrix = data.frame(word= as.character(names(ID_matrix)), freq= ID_matrix)
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dlalgroup
parents:
diff changeset
272 colnames(ID_matrix) = c("word", "freq")
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dlalgroup
parents:
diff changeset
273 ID_matrix = ID_matrix[ID_matrix$freq == 1,]
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
274
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
275 plotWordCloud(ID_matrix,
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
276 max.words = min(nrow(ID_matrix),input$nword),
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
277 scale= c(input$fontsize/10, input$fontsize/10),
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
278 colors= brewer.pal(8,"Greys")[4:8])
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dlalgroup
parents:
diff changeset
279 })
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
280
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
281 output$downloadWordcloud <- downloadHandler(
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
282 filename = function() {
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
283 paste0(paste0("Wordcloudof",data[[colindex_id]][index_ID()]),".pdf", sep="")
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
284 },
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
285 content = function(file) {
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
286 ID_matrix = matrix[index_ID(),]
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
287 ID_matrix = data.frame(word= names(ID_matrix), freq= ID_matrix)
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
288 colnames(ID_matrix) = c("word", "freq")
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
289 ID_matrix = ID_matrix[ID_matrix$freq == 1,]
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dlalgroup
parents:
diff changeset
290
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
291 pdf(file)
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
292 plotWordCloud(ID_matrix,
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
293 max.words = min(max(nrow(ID_matrix)),input$nword),
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
294 scale= c(input$fontsize/10, input$fontsize/10),
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
295 colors= brewer.pal(8,"Greys")[4:8])
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dlalgroup
parents:
diff changeset
296 dev.off()
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dlalgroup
parents:
diff changeset
297 }
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dlalgroup
parents:
diff changeset
298 )
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
299
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
300 ##### Table #####
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
301 output$Table <- renderText({
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
302 paste("Most occuring words among IDs")
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
303 })
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
304
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
305 output$datatable <- DT::renderDataTable({
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
306
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
307 colsum_data= data.frame(word=colnames(matrix), freq=colSums(matrix))
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
308 colsum_data = colsum_data[order(colsum_data$freq, decreasing = T),]
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
309 colnames(colsum_data) = c("Word", paste0("IDs (total n=", nrow(matrix),")"))
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
310
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
311 DT::datatable(colsum_data,
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
312 extensions = c("Buttons"),
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
313 rownames = F,
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
314 fillContainer = T,
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
315 escape=FALSE,
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
316 options = list(dom = "t",
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
317 scrollY = min(nrow(colsum_data),500),
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
318 scrollX= TRUE,
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
319 scroller = TRUE,
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
320 autoWidth = TRUE,
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
321 pageLength = nrow(colsum_data),
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
322 columnDefs = list(list(className = 'dt-center', targets = "_all"),
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
323 list(width = '50%', targets = "_all")))
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
324 )
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
325 })
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
326
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
327 ##### Colour/Grouping #####
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
328
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
329 outVar <- reactive({
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
330 if(input$colour == "Grouping variable"){
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
331 return(names(data)[index_grouping])
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
332 } else {
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
333 return(colnames(matrix))
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
334 }
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
335 })
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
336
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
337 observe({
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
338 updateSelectInput(session, "colour_select", choices = outVar())})
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
339
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
340 colour_choice = reactive({
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
341 if(input$colour == "Grouping variable"){
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
342 return(as.factor(data[,input$colour_select]))
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
343 } else {
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
344 matrix = as.data.frame(matrix)
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
345 colour_byword = matrix[[input$colour_select]]
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
346 colour_byword = ifelse(colour_byword > 0,"Selected word associated with ID","Selected word not associated with ID")
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
347 return(as.factor(colour_byword))
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
348 }
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
349 })
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
350
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
351 color_palette = reactive({palette=c("#A6CEE3", "#1F78B4", "#B2DF8A", "#33A02C", "#FB9A99",
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
352 "#E31A1C", "#FDBF6F", "#FF7F00", "#CAB2D6", "#6A3D9A",
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
353 "#00AFBB", "#E7B800", "#FC4E07", "#999999", "#E69F00",
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
354 "#56B4E9", "#009E73", "#F0E442", "#0072B2", "#D55E00")
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
355 return( palette[1:length(levels(colour_choice()))] )
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
356 })
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
357
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
358 ##### Dimension reduction plot and download #####
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
359
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
360 data.dimred = reactive({
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
361 if (input$method == "t-SNE"){
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
362 tsne_result <- Rtsne(matrix, perplexity = input$perplexity, check_duplicates=F)
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
363 data["X_Coord"] = tsne_result$Y[,1]
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
364 data["Y_Coord"] = tsne_result$Y[,2]
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
365 return(data)
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
366 } else if (input$method == "UMAP"){
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
367 umap_result = umap(matrix)
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
368 data["X_Coord"] = umap_result$layout[,1]
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
369 data["Y_Coord"] = umap_result$layout[,2]
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
370 return(data)
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
371 }
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
372 })
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
373
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
374 output$TsnePlot <- renderPlotly({
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
375
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
376 if (input$label == "Index") {
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
377 labeling = as.character(seq(1,nrow(data)))
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
378 } else if (input$label == "IDs") {
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
379 labeling= as.character(data[[colindex_id]])
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
380 }
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
381
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
382 p = plot_ly(colors = color_palette()) %>%
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
383 add_trace(type="scatter",
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
384 mode = 'markers',
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
385 x = data.dimred()$X_Coord[index_ID()],
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
386 y = data.dimred()$Y_Coord[index_ID()],
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
387 opacity=0.15,
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
388 marker = list(
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
389 color = "grey",
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
390 size = 80)) %>%
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
391 add_trace(x=data.dimred()$X_Coord,
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
392 y=data.dimred()$Y_Coord,
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
393 type="scatter",
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
394 mode="text",
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
395 text= labeling,
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
396 textfont = list(size= input$labelsize),
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
397 color = factor(colour_choice())) %>%
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
398 add_trace(x=data.dimred()$X_Coord,
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
399 y=data.dimred()$Y_Coord,
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
400 type="scatter",
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
401 mode="markers",
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
402 opacity=0,
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
403 text= paste0( "ID: ",data[[colindex_id]], "\n",
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
404 "Index: ",seq(1,nrow(data)), "\n",
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
405 "Grouping: ", paste(data[,index_grouping])),
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
406 hoverinfo = "text",
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
407 color = factor(colour_choice())) %>%
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
408 layout(showlegend = FALSE,
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
409 yaxis= list(title = "",
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
410 zeroline = FALSE,
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
411 linecolor = toRGB("black"),
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
412 linewidth = 1,
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
413 showticklabels = FALSE,
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
414 showgrid = FALSE),
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
415 xaxis = list(title = "",
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
416 zeroline = FALSE,
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
417 linecolor = toRGB("black"),
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
418 linewidth = 1,
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
419 showticklabels = FALSE,
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
420 showgrid = FALSE),
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
421 autosize = T) %>%
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
422 config(modeBarButtonsToRemove = c("zoomIn2d", "zoomOut2d", "hoverClosestGeo", "hoverClosestGl2d", "toImage",
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
423 "hoverClosestCartesian", "lasso2d", "select2d", "resetScale2d",
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
424 "hoverCompareCartesian", "hoverClosestPie", "toggleSpikelines"), displaylogo = FALSE) %>%
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
425 style(hoverinfo = "none", traces = c(1,2))
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
426
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
427 p
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
428 })
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
429
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
430 #legend of plotly plot by ggplot
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
431
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
432 output$TsnePlot_legend <- renderPlot({
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
433 p = ggplot(data, aes(x=1, y=1)) +
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
434 geom_text(aes(label=seq(1,nrow(data)), colour=factor(colour_choice())),
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
435 size=3.5, fontface = "bold") +
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
436 theme_classic()+
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
437 scale_color_manual(values = color_palette())+
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
438 theme(legend.title = element_blank())+
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
439 theme(legend.position = "right")+
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
440 theme(legend.text=element_text(size=9))
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
441 leg <- get_legend(p)
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
442 as_ggplot(leg)
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
443 })
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
444
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
445 output$downloadPlotdata <- downloadHandler(
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
446 filename = function() {
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
447 paste0(input$method,"_coordinates.csv")
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
448 },
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
449 content = function(file) {
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
450 write.csv(data.dimred(), file, row.names = F)
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
451 }
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
452 )
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
453
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
454 ##### Hierarchical clustering #######
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
455
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
456 output$hclust <- renderPlot({
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
457 set.seed(42)
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
458 clustering=hclust(dist(matrix), method=input$hcmethod)
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
459 par(oma=c(3,3,3,3))
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
460 palette(color_palette())
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
461 par(mar = rep(0, 4))
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
462 myplclust(clustering,
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
463 labels=paste(data[[colindex_id]]),
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
464 lab.col=as.fumeric(as.character(colour_choice()), levels = sort(unique(as.character(colour_choice())))),
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
465 cex=as.numeric(input$labelsize_hc/10),
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
466 main="",
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
467 yaxt="n",
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
468 ylab= "")
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
469 })
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
470
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
471 #legend
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
472 output$hclust_legend <- renderPlot({
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
473 p = ggplot(data, aes(x=1, y=1)) +
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
474 geom_text(aes(label=seq(1,nrow(data)), colour=factor(colour_choice())), fontface = "bold") +
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
475 theme_classic()+
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
476 scale_color_manual(values = color_palette())+
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
477 theme(legend.title = element_blank())+
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
478 theme(legend.position = "right")+
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
479 theme(legend.text=element_text(size=9))
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
480 leg <- get_legend(p)
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
481 as_ggplot(leg)
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
482 })
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
483
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
484
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
485 ##### Test field for development ######
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
486 #output$test <- renderPrint({
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
487 #})
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
488
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
489 }
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
490
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
491 ###### APP ######
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
492 shinyApp(ui, server)