changeset 4:8e17c31c536a draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
author artbio
date Thu, 11 Jul 2019 12:31:28 -0400
parents 8e44c9e18a56
children 569334568afa
files high_dim_visu.R high_dim_visu.xml test-data/hcpc-2.coord.tab test-data/hcpc-2.labels.pdf test-data/hcpc-3.coord.tab test-data/hcpc-3.labels.pdf test-data/hcpc.clusters.tab test-data/hcpc.factor.extval.txt test-data/hcpc.labels.pdf test-data/hcpc.nolabels.factor.pdf test-data/hcpc.nolabels.pdf test-data/numeric_factor.tsv test-data/pca.2vs3.pdf test-data/pca.coord.pdf test-data/pca.coord.tab test-data/pca.labels.pdf test-data/pca.nolabels.2-lev-factor.pdf test-data/pca.nolabels.factors.pdf test-data/pca.nolabels.numerical-factor.pdf test-data/pca.nolabels.pdf test-data/tsne-2.coord.tab test-data/tsne-2.nolabels.pdf test-data/tsne.labels.factor.pdf test-data/tsne.labels.pdf test-data/tsne.nolabels.pdf
diffstat 25 files changed, 6458 insertions(+), 4208 deletions(-) [+]
line wrap: on
line diff
--- a/high_dim_visu.R	Thu Jun 27 06:17:08 2019 -0400
+++ b/high_dim_visu.R	Thu Jul 11 12:31:28 2019 -0400
@@ -11,7 +11,7 @@
 library(ggplot2)
 library(ggfortify)
 library(RColorBrewer)
-
+library(ClusterR)
 
 # Arguments
 option_list = list(
@@ -92,13 +92,13 @@
     default = 1.0,
     type = 'numeric',
     help = "theta [default : '%default' ]"
-  ), 
+  ),
   make_option(
     "--Rtsne_max_iter",
     default = 1000,
     type = 'integer',
     help = "max_iter [default : '%default' ]"
-  ), 
+  ),
   make_option(
     "--Rtsne_pca",
     default = TRUE,
@@ -128,13 +128,25 @@
     default = 12.0,
     type = 'numeric',
     help = " Exaggeration factor used to multiply the P matrix in the first part of the optimization [default : '%default' ]"
-  ), 
+  ),
    make_option(
     "--PCA_npc",
     default = 5,
     type = 'integer',
     help = "number of dimensions kept in the results [default : '%default' ]"
   ),
+   make_option(
+    "--PCA_x_axis",
+    default = 1,
+    type = 'integer',
+    help = "PC to plot in the x axis [default : '%default' ]"
+  ),
+   make_option(
+    "--PCA_y_axis",
+    default = 2,
+    type = 'integer',
+    help = "PC to plot in the y axis [default : '%default' ]"
+  ),
   make_option(
     "--HCPC_ncluster",
     default = -1,
@@ -200,7 +212,19 @@
     default = -1,
     type = 'numeric',
     help = "The maximum number of iterations for the consolidation [default :'%default']"
-  ) 
+  ),
+  make_option(
+    "--HCPC_clust",
+    default = "",
+    type = 'character',
+    help = "Output result of HCPC clustering : two column table (cell identifiers and clusters) [default :'%default']"
+  ),
+  make_option(
+    "--mutual_info",
+    default = "",
+    type = "character",
+    help = "Output file of external validation of HCPC clustering with factor levels [default :'%default']"
+  )
 )
 
 opt = parse_args(OptionParser(option_list = option_list),
@@ -211,6 +235,43 @@
 if(opt$HCPC_max == -1) {opt$HCPC_max <- NULL}
 if(opt$HCPC_kk == -1) {opt$HCPC_kk <- Inf}
 
+##Add legend to plot()
+legend.col <- function(col, lev){
+
+opar <- par
+
+n <- length(col)
+
+bx <- par("usr")
+
+box.cx <- c(bx[2] + (bx[2] - bx[1]) / 1000,
+bx[2] + (bx[2] - bx[1]) / 1000 + (bx[2] - bx[1]) / 50)
+box.cy <- c(bx[3], bx[3])
+box.sy <- (bx[4] - bx[3]) / n
+
+xx <- rep(box.cx, each = 2)
+
+par(xpd = TRUE)
+for(i in 1:n){
+
+yy <- c(box.cy[1] + (box.sy * (i - 1)),
+box.cy[1] + (box.sy * (i)),
+box.cy[1] + (box.sy * (i)),
+box.cy[1] + (box.sy * (i - 1)))
+polygon(xx, yy, col = col[i], border = col[i])
+
+}
+par(new = TRUE)
+plot(0, 0, type = "n",
+ylim = c(min(lev), max(lev)),
+yaxt = "n", ylab = "",
+xaxt = "n", xlab = "",
+frame.plot = FALSE)
+axis(side = 4, las = 2, tick = FALSE, line = .25)
+par <- opar
+}
+
+
 data = read.table(
   opt$data,
   check.names = FALSE,
@@ -228,20 +289,24 @@
   rownames(contrasting_factor) <- contrasting_factor[,1]
   contrasting_factor <- contrasting_factor[colnames(data),]
   colnames(contrasting_factor) <- c("id","factor")
-  contrasting_factor$factor <- as.factor(contrasting_factor$factor)
-  if(nlevels(contrasting_factor$factor) == 2){
-    colors_labels <- c("#E41A1C", "#377EB8")
+  if(is.numeric(contrasting_factor$factor)){
+    factor_cols <- rev(brewer.pal(n = 11, name = "RdYlGn"))[contrasting_factor$factor]
   } else {
-    colors_labels <- brewer.pal(nlevels(contrasting_factor$factor), name = 'Paired')
+    contrasting_factor$factor <- as.factor(contrasting_factor$factor)
+    if(nlevels(contrasting_factor$factor) == 2){
+      colors_labels <- c("#E41A1C", "#377EB8")
+    } else {
+      colors_labels <- brewer.pal(nlevels(contrasting_factor$factor), name = 'Paired')
+    }
+    factorColors <-
+      with(contrasting_factor,
+           data.frame(factor = levels(contrasting_factor$factor),
+                      color = I(colors_labels)
+           )
+      )
+    factor_cols <- factorColors$color[match(contrasting_factor$factor,
+                                          factorColors$factor)]
   }
-  factorColors <-
-    with(contrasting_factor,
-         data.frame(factor = levels(contrasting_factor$factor),
-                    color = I(colors_labels)
-         )
-    )
-  factor_cols <- factorColors$color[match(contrasting_factor$factor,
-                                          factorColors$factor)]
 } else {
   factor_cols <- rep("deepskyblue4", length(rownames(data)))
 }
@@ -272,19 +337,24 @@
     ggplot(embedding, aes(x=V1, y=V2)) +
       geom_point(size=1, color='deepskyblue4') +
       gg_legend +
-      xlab("") +
-      ylab("") +
+      xlab("t-SNE 1") +
+      ylab("t-SNE 2") +
       ggtitle('t-SNE') +
       if (opt$labels) {
         geom_text(aes(label=Class),hjust=-0.2, vjust=-0.5, size=1.5, color='deepskyblue4')
       }
     } else {
-    embedding$factor <- as.factor(contrasting_factor$factor)
+    if(is.numeric(contrasting_factor$factor)){
+      embedding$factor <- contrasting_factor$factor
+    } else {
+      embedding$factor <- as.factor(contrasting_factor$factor)
+    }
+
     ggplot(embedding, aes(x=V1, y=V2, color=factor)) +
       geom_point(size=1) + #, color=factor_cols
       gg_legend +
-      xlab("") +
-      ylab("") +
+      xlab("t-SNE 1") +
+      ylab("t-SNE 2") +
       ggtitle('t-SNE') +
       if (opt$labels) {
         geom_text(aes(label=Class, colour=factor),hjust=-0.2, vjust=-0.5, size=1.5)
@@ -294,7 +364,7 @@
   
   #save coordinates table
   if(opt$table_coordinates != ''){
-  coord_table <- cbind(rownames(tdf),as.data.frame(tsne_out$Y))
+  coord_table <- cbind(rownames(tdf), round(as.data.frame(tsne_out$Y), 6))
   colnames(coord_table)=c("Cells",paste0("DIM",(1:opt$Rtsne_dims)))
   }
 }
@@ -305,20 +375,24 @@
   pca <- PCA(t(data), ncp=opt$PCA_npc, graph=FALSE)
   pdf(opt$pdf_out)
   if (opt$labels == FALSE) {
-    plot(pca, label="none" , col.ind = factor_cols)
+    plot(pca, axes = c(opt$PCA_x_axis,opt$PCA_y_axis), label="none" , col.ind = factor_cols)
     } else {
-    plot(pca, cex=0.2 , col.ind = factor_cols)
+    plot(pca, axes = c(opt$PCA_x_axis,opt$PCA_y_axis), cex=0.2 , col.ind = factor_cols)
   }
 if (opt$factor != '') {
+  if(is.factor(contrasting_factor$factor)) {
     legend(x = 'topright', 
        legend = as.character(factorColors$factor),
        col = factorColors$color, pch = 16, bty = 'n', xjust = 1, cex=0.7)
+  } else {
+    legend.col(col = rev(brewer.pal(n = 11, name = "RdYlGn")), lev = cut(contrasting_factor$factor, 11, label = FALSE))
+  }
 }
 dev.off()
 
   #save coordinates table
   if(opt$table_coordinates != ''){
-  coord_table <- cbind(rownames(pca$ind$coord),as.data.frame(pca$ind$coord))
+  coord_table <- cbind(rownames(pca$ind$coord), round(as.data.frame(pca$ind$coord), 6))
   colnames(coord_table)=c("Cells",paste0("DIM",(1:opt$PCA_npc)))
   }
 
@@ -355,11 +429,25 @@
 
 # user contrasts on the pca
 if (opt$factor != '') {
-    plot(pca, label="none", habillage="ind", col.hab=factor_cols)
+  plot(pca, label="none", col.ind = factor_cols)
+  if(is.factor(contrasting_factor$factor)) {
     legend(x = 'topright', 
        legend = as.character(factorColors$factor),
        col = factorColors$color, pch = 16, bty = 'n', xjust = 1, cex=0.7)
-    }
+    
+    ## Normalized Mutual Information
+    sink(opt$mutual_info)
+    res <- external_validation(
+       true_labels = as.numeric(contrasting_factor$factor),
+       clusters = as.numeric(res.hcpc$data.clust$clust),
+       summary_stats = TRUE
+    )
+    sink()
+
+  } else {
+    legend.col(col = rev(brewer.pal(n = 11, name = "RdYlGn")), lev = cut(contrasting_factor$factor, 11, label = FALSE))
+  }
+}
 ## Clusters to which individual observations belong # used ?
 # Clust <- data.frame(Cluster = res.hcpc$data.clust[, (nrow(data) + 1)],
 #                     Observation = rownames(res.hcpc$data.clust))
@@ -380,21 +468,22 @@
 # Sil = fviz_silhouette(hc.cut)
 # sil1 = as.data.frame(Sil$data)
 
-## Normalized Mutual Information # to be implemented later
-# sink(opt$mutual_info)
-# res = external_validation(
-#   as.numeric(factor(metadata[, Patient])),
-#   as.numeric(metadata$Cluster),
-#   method = "adjusted_rand_index",
-#   summary_stats = TRUE
-# )
-# sink()
 dev.off()
 
  if(opt$table_coordinates != ''){
-  coord_table <- cbind(Cell=rownames(res.hcpc$call$X),as.data.frame(res.hcpc$call$X))
+  coord_table <- cbind(Cell=rownames(res.hcpc$call$X),
+                       round(as.data.frame(res.hcpc$call$X[, -length(res.hcpc$call$X)]), 6),
+                       as.data.frame(res.hcpc$call$X[, length(res.hcpc$call$X)])
+                       )
   colnames(coord_table)=c("Cells",paste0("DIM",(1:opt$HCPC_npc)),"Cluster")
   }
+
+ if(opt$HCPC_clust != ""){
+ res_clustering <- data.frame(Cell = rownames(res.hcpc$data.clust),
+                              Cluster = res.hcpc$data.clust$clust)
+ 
+ }
+
 }
 
 ## Return coordinates file to user
@@ -411,7 +500,16 @@
 }
 
 
-  
+if(opt$HCPC_clust != ""){
+  write.table(
+    res_clustering,
+    file = opt$HCPC_clust,
+    sep = "\t",
+    quote = F,
+    col.names = T,
+    row.names = F
+    )
+}  
 
 
 
--- a/high_dim_visu.xml	Thu Jun 27 06:17:08 2019 -0400
+++ b/high_dim_visu.xml	Thu Jul 11 12:31:28 2019 -0400
@@ -1,12 +1,12 @@
-<tool id="high_dimensions_visualisation" name="Generate PCA, tSNE and HCPC" version="0.9.3">
+<tool id="high_dimensions_visualisation" name="Generate PCA, tSNE and HCPC" version="0.9.4">
     <description>from highly dimensional expression data</description>
     <requirements>
-        <requirement type="package" version="1.3.2=r3.3.2_0">r-optparse</requirement>
-        <requirement type="package" version="1.39=r3.3.2_0">r-factominer</requirement>
-        <requirement type="package" version="1.0.5=r3.3.2_0">r-factoextra</requirement>
-        <requirement type="package" version="0.13=r3.3.2_0">r-rtsne</requirement>
-        <requirement type="package" version="2.2.1=r3.3.2_0">r-ggplot2</requirement>
-        <requirement type="package" version="0.4.1=r3.3.2_0">r-ggfortify</requirement>
+        <requirement type="package" version="1.6.2=r35h6115d3f_0">r-optparse</requirement>
+        <requirement type="package" version="1.42=r35h6115d3f_0">r-factominer</requirement>
+        <requirement type="package" version="1.0.5">r-factoextra</requirement>
+        <requirement type="package" version="0.15=r351he1b5a44_0">r-rtsne</requirement>
+        <requirement type="package" version="0.4.7=r351h6115d3f_0">r-ggfortify</requirement>
+        <requirement type="package" version="1.1.9=r351h0357c0b_0">r-clusterr</requirement>
     </requirements>
     <stdio>
         <exit_code range="1:" level="fatal" description="Tool exception" />
@@ -53,13 +53,21 @@
                 --HCPC_max '$visualisation.HCPC_max'
                 --HCPC_clusterCA '$visualisation.HCPC_clusterCA'
                 --HCPC_kk '$visualisation.HCPC_kk'
+                #if $visualisation.res_clustering == "yes":
+                    --HCPC_clust '$HCPC_clust'
+                #end if 
             #end if
             
             #if $visualisation.visu_choice == "PCA":
                 --PCA_npc '$visualisation.PCA_npc'
+                --PCA_x_axis '$visualisation.PCA_x_axis'
+                --PCA_y_axis '$visualisation.PCA_y_axis'
             #end if
             
-           
+            #if $visualisation.visu_choice == "HCPC" and $factor_condition.factor_choice == "Yes":
+                --mutual_info '$mutual_info'
+            #end if            
+
             --pdf_out '$pdf_out'
             
 ]]></command>
@@ -111,10 +119,10 @@
 					<option value="TRUE">Yes</option>
 					<option value="FALSE" selected="true">False</option>
 				</param>
-				<param name="Rtsne_normalize"  type="select" label="Normalisation of data"
-				             help="Should variables (gene expressions) be normalized internally prior to distance calculations? " > 
-					<option value="TRUE" selected="true">Yes</option>
-					<option value="FALSE">False</option>
+				<param name="Rtsne_normalize"  type="select" label="Normalisation of data"	
+				             help="Should variables (gene expressions) be normalized internally prior to distance calculations? " > 	
+					<option value="TRUE" selected="true">Yes</option>	
+					<option value="FALSE">False</option>	
 				</param>
                 <param name="Rtsne_perplexity" value="10.0" type="float" label="perplexity (t-SNE)" help="should be less than ((nbr observations)-1)/3" /> 
                 <param name="Rtsne_theta" value="1.0" type="float" label="theta (t-SNE)"/>
@@ -154,9 +162,15 @@
 				</param>
 				 <param name="HCPC_kk" value="-1" type="text" label="kk, Number of clusters used in a Kmeans preprocessing "
                        help="No k-means consolidation is done if a kk value is provided (default=-1)" />
+                <param label="Return HCPC clustering table" name="res_clustering" type="select">
+                    <option value="no" selected="True">No</option>
+                    <option value="yes">Yes</option>
+                </param>
             </when>
             <when value="PCA">
             	  <param name="PCA_npc" value="5" type="integer" label="Number of principal components to keep" help="The number of dimensions which are kept for PCA analysis (default=5)" />
+                  <param name="PCA_x_axis" value="1" type="integer" label="First principal component to plot" help="X axis for PCA plot (default=1)" />
+                  <param name="PCA_y_axis" value="2" type="integer" label="Second principal component to plot" help="Y axis for PCA plot (default=2)" />
             </when>
         </conditional>
             <param label="Return scatter plot table coordinates" name="coord" type="select">
@@ -170,6 +184,12 @@
         <data name="table_coordinates" format="tabular" label="Scatter plot coordinates from ${visualisation.visu_choice} of ${on_string}" >
             <filter>coord == 'yes'</filter>
         </data>
+        <data name="mutual_info" format="txt" label="External validation of clustering from ${visualisation.visu_choice} of ${on_string}" >
+            <filter>visualisation['visu_choice'] == 'HCPC' and factor_condition['factor_choice'] == 'Yes'</filter>
+        </data>
+        <data name="HCPC_clust" format="tabular" label="Clustering table from ${visualisation.visu_choice} of ${on_string}" >
+            <filter>visualisation['visu_choice'] == 'HCPC' and visualisation['res_clustering'] == 'yes'</filter>
+        </data>
     </outputs>
     <tests>
         <!-- test PCA -->
@@ -187,6 +207,17 @@
             <param name="factor_choice" value="No" />
             <output name="pdf_out" file="pca.nolabels.pdf" ftype="pdf"/>
         </test>
+        <!-- test PCA PC2 vs PC3 -->
+        <test>
+            <param name="input" value="cpm_input.tsv" ftype="txt"/>
+            <param name="labels" value="no" />
+            <param name="visu_choice" value="PCA" />
+            <param name="factor_choice" value="No" />
+            <param name="PCA_x_axis" value="2" />
+            <param name="PCA_y_axis" value="3" />
+            <output name="pdf_out" file="pca.2vs3.pdf" ftype="pdf"/>
+        </test>
+
         <!-- test Coordinates tables on PCA -->
         <test>
             <param name="input" value="cpm_input.tsv" ftype="txt"/>
@@ -213,7 +244,16 @@
             <param name="visu_choice" value="PCA" />
             <param name="factor_choice" value="Yes" />
             <param name="factor" value="2-lev_factor.tsv" ftype="txt"/>
-            <output name="pdf_out" file="pca.nolabels.2-lev-factor.pdf" ftype="pdf"/>
+            <output name="pdf_out" file="pca.nolabels.2-lev-factor.pdf" compare="sim_size" ftype="pdf"/>
+        </test>
+        <!-- test numerical factor contrasting on PCA -->
+        <test>
+            <param name="input" value="cpm_input.tsv" ftype="txt"/>
+            <param name="labels" value="no" />
+            <param name="visu_choice" value="PCA" />
+            <param name="factor_choice" value="Yes" />
+            <param name="factor" value="numeric_factor.tsv" ftype="txt"/>
+            <output name="pdf_out" file="pca.nolabels.numerical-factor.pdf" compare="sim_size" ftype="pdf"/>
         </test>
         <test>
             <param name="input" value="cpm_input.tsv" ftype="txt"/>
@@ -221,7 +261,7 @@
             <param name="visu_choice" value="PCA" />
             <param name="factor_choice" value="Yes" />
             <param name="factor" value="shuffled_factor.tsv" ftype="txt"/>
-            <output name="pdf_out" file="pca.nolabels.factors.pdf" ftype="pdf"/>
+            <output name="pdf_out" file="pca.nolabels.factors.pdf" compare="sim_size" ftype="pdf"/>
         </test>
         <!-- test HCPC -->
         <test>
@@ -230,7 +270,7 @@
             <param name="visu_choice" value="HCPC" />
             <param name="HCPC_npc" value="5"/>
             <param name="HCPC_ncluster" value="-1"/>
-            <output name="pdf_out" file="hcpc.labels.pdf" ftype="pdf"/>
+            <output name="pdf_out" file="hcpc.labels.pdf" compare="sim_size" ftype="pdf"/>
         </test>
         <!-- test factor contrasting on HCPC -->
         <test>
@@ -239,9 +279,12 @@
             <param name="visu_choice" value="HCPC" />
             <param name="HCPC_npc" value="5"/>
             <param name="HCPC_ncluster" value="-1"/>
+            <param name="res_clustering" value="yes"/>
             <param name="factor_choice" value="Yes" />
             <param name="factor" value="factor.tsv" ftype="txt"/>
-            <output name="pdf_out" file="hcpc.nolabels.factor.pdf" ftype="pdf"/>
+            <output name="pdf_out" file="hcpc.nolabels.factor.pdf" compare="sim_size" ftype="pdf"/>
+            <output name="mutual_info" file="hcpc.factor.extval.txt" ftype="txt"/>
+            <output name="HCPC_clust" file="hcpc.clusters.tab" ftype="tabular"/>
         </test>
         <test>
             <param name="input" value="cpm_input.tsv" ftype="txt"/>
@@ -249,7 +292,7 @@
             <param name="HCPC_npc" value="5"/>
             <param name="HCPC_ncluster" value="-1"/>
             <param name="visu_choice" value="HCPC" />
-            <output name="pdf_out" file="hcpc.nolabels.pdf" ftype="pdf"/>
+            <output name="pdf_out" file="hcpc.nolabels.pdf" compare="sim_size" ftype="pdf"/>
         </test>
         <test>
             <param name="input" value="cpm_input.tsv" ftype="txt"/>
@@ -271,7 +314,7 @@
             <param name="HCPC_metric" value="euclidian"/>
             <param name="HCPC_npc" value="4" />
             <param name="HCPC_clusterCA" value="cols" />
-            <output name="pdf_out" file="hcpc-3.labels.pdf" ftype="pdf"/>
+            <output name="pdf_out" file="hcpc-3.labels.pdf" compare="sim_size" ftype="pdf"/>
             <output name="table_coordinates" file="hcpc-3.coord.tab" ftype="tabular"/>
         </test>
         <!-- test t-SNE -->
@@ -282,7 +325,7 @@
             <param name="Rtsne_seed" value="49"/>
             <param name="Rtsne_perplexity" value="10"/>
             <param name="Rtsne_theta" value="1" />
-            <output name="pdf_out" file="tsne.labels.pdf" ftype="pdf"/>
+            <output name="pdf_out" file="tsne.labels.pdf" ftype="pdf" compare="sim_size" delta="500"/>
         </test>
         <test>
             <param name="input" value="cpm_input.tsv" ftype="txt"/>
@@ -291,22 +334,9 @@
             <param name="Rtsne_seed" value="49"/>
             <param name="Rtsne_perplexity" value="10"/>
             <param name="Rtsne_theta" value="1" />
-            <output name="pdf_out" file="tsne.nolabels.pdf" ftype="pdf"/>
+            <output name="pdf_out" file="tsne.nolabels.pdf" ftype="pdf" compare="sim_size" delta="500"/>
         </test>
-       	<test>
-            <param name="input" value="cpm_input.tsv" ftype="txt"/>
-            <param name="labels" value="no" />
-            <param name="visu_choice" value="tSNE" />
-            <param name="coord" value="yes" />
-            <param name="Rtsne_seed" value="42"/>
-            <param name="Rtsne_perplexity" value="5.0"/>
-            <param name="Rtsne_theta" value="1.0" />
-            <param name="Rtsne_dims" value="3" />
-            <param name="Rtsne_exaggeration_factor" value="15.0" />
-            <output name="pdf_out" file="tsne-2.nolabels.pdf" ftype="pdf"/>
-            <output name="table_coordinates" file="tsne-2.coord.tab" ftype="tabular"/>
-        </test>
-        <!-- test factor contrasting on t-SNE -->
+                <!-- test factor contrasting on t-SNE -->
         <test>
             <param name="input" value="cpm_input.tsv" ftype="txt"/>
             <param name="labels" value="yes" />
@@ -316,7 +346,20 @@
             <param name="Rtsne_seed" value="49"/>
             <param name="Rtsne_perplexity" value="10"/>
             <param name="Rtsne_theta" value="1" />
-            <output name="pdf_out" file="tsne.labels.factor.pdf" ftype="pdf"/>
+            <output name="pdf_out" file="tsne.labels.factor.pdf" ftype="pdf" compare="sim_size" delta="500"/>
+        </test>
+       	<test>
+            <param name="input" value="cpm_input.tsv" ftype="txt"/>
+            <param name="labels" value="no" />
+            <param name="visu_choice" value="tSNE" />
+            <param name="Rtsne_seed" value="49" />
+            <param name="coord" value="yes" />
+            <param name="Rtsne_dims" value="3" />
+            <param name="Rtsne_perplexity" value="10"/>
+            <param name="Rtsne_theta" value="1" />
+            <param name="Rtsne_normalize" value="FALSE" />
+            <output name="pdf_out" file="tsne-2.nolabels.pdf" ftype="pdf" compare="sim_size" delta="500"/>
+            <output name="table_coordinates" file="tsne-2.coord.tab" ftype="tabular" compare="sim_size" delta="500"/>
         </test>
     </tests>
     <help>
@@ -339,19 +382,31 @@
 
 * Principal Components Analysis (PCA)
 * Hierarchical Clustering of Principal Components (HCPC)
-* t-distributed Stochastic Neighbor Embedding
+* t-distributed Stochastic Neighbor Embedding (t-SNE)
 
 The tool returns in addition the table of the coordinates of the observations (eg RNAseq libraries)
 in the low dim space, which can be used for post-treatment or to further adjust the provided visualisation.
 
+If HCPC is used, this tool can also return the clustering table. It contains two columns of n observations :
+
+* Observation labels
+* Cluster labels
+
 ** Contrast data with a factor **
 The tool offers the possibility to colour data points according to the levels of a factor.
 To use the option "Factor to contrast data", provide a tabulated-separated, two-column table
 with first column containing the cell/data library identifiers (same identifiers as those
 provided as column headers in the input data table) and second column containing the corresponding
-factor levels value. This table does not need to be sorted in the same order as in the data
+factor levels value (if this vector is numerical, then the color palette used is quantitative). 
+This table does not need to be sorted in the same order as in the data
 table. It may also contain more identifiers than those provided in the data table.
 
+If HCPC visualisation and constrasting data are chosen, an additional text file is given. It contains
+several metrics of external validation of clustering. It will compare the capacity of HCPC clustering
+to recreate classes contained in the factor data file. If the constrasting factor is quantitative,
+the file will be empty. 
+
+
     </help>
     <citations>
         <citation type="bibtex">@Article{,
@@ -381,5 +436,14 @@
             url = {https://github.com/jkrijthe/Rtsne},
             }
         </citation>
+        <citation type="bibtex">@Manual{,
+            title = {{ClusterR}: Gaussian Mixture Models, K-Means, Mini-Batch-Kmeans,
+            K-Medoids and Affinity Propagation Clustering},
+            author = {Lampros Mouselimis},
+            year = {2019},
+            note = {R package version 1.1.9},
+            url = {https://github.com/mlampros/ClusterR},
+            }
+        </citation>
   </citations>
 </tool>
--- a/test-data/hcpc-2.coord.tab	Thu Jun 27 06:17:08 2019 -0400
+++ b/test-data/hcpc-2.coord.tab	Thu Jul 11 12:31:28 2019 -0400
@@ -1,1034 +1,1034 @@
 Cells	DIM1	DIM2	DIM3	DIM4	Cluster
-1001000015.B2	-11.5652657867278	-1.31380578757931	-0.0153340976851289	-0.248070111266024	1
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-1001000031.F2	-10.9034865985644	0.356152065721901	-1.17963279262154	0.684246722251061	1
-1001000037.A4	-10.8022433351516	-0.173306230238628	-1.10393520337389	-2.29592847917511	1
-1001000250.B4	-10.7583812375057	-2.52739546376501	-0.162642559907488	-2.6771648328183	1
-1001000174.C6	-10.5475015195375	-0.548848108446587	-1.0068785965758	-1.26609484454219	1
-1001000012.G9	-10.5212024621584	1.40339679845456	-0.61743868486739	-0.233496247865159	1
-1001000017.F7	-10.2602641871214	-1.02343788487437	0.731991442159092	-0.0631679225716421	1
-1001000259.G12	-10.2480311840355	0.259957606293954	0.616282421244151	-2.52535933167469	1
-1001000037.F4	-10.1480892559435	-1.4496493487958	0.704473039249547	0.452106896129478	1
-1001000037.A5	-10.1342852049663	-0.7513022112645	-0.388441937637595	0.0232244211500611	1
-1001000182.C10	-10.1303449816973	-2.70598522544537	0.35536845991631	-1.37090840645819	1
-1001000245.B4	-9.98089109936251	-0.464210382352047	-1.17893224904116	-1.20644427203249	1
-1001000012.E6	-9.97477143632224	1.86222430890467	0.60233900433345	-0.793617681384475	1
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-1001000037.B7	-9.60773070986632	-0.937836380747054	1.3900392051156	0.36809573969286	1
-1001000258.G10	-9.58069795669186	2.26104805942392	0.435414628399747	-1.13890407382671	1
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-1001000037.A1	-9.07862937647765	0.0596669579741007	1.69217448762322	0.564204105297967	1
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-1001000267.B8	-8.88748990078065	-2.62254321281974	-0.443848514870762	-2.97946666414132	1
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-1001000037.C3	-8.87896390177549	-2.52741460508887	0.35173770777012	0.797361520801759	1
-1001000037.E11	-8.87510871504548	-2.48089924006473	0.408222021073352	-0.075358888154139	1
-1001000037.E7	-8.87193070481487	-1.94720182479431	3.07993212311602	3.0812567218477	1
-1001000012.C5	-8.86103768667453	-0.909878703251286	1.32577024866918	1.58126198765515	1
-1001000037.H4	-8.83837237036198	-0.893761282478489	0.403701883042241	0.446850072585765	1
-1001000012.D11	-8.82589115401337	0.466553269629413	0.563698191370276	1.4868026984566	1
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-1001000174.D5	-8.67889883298171	-1.38293204798523	-0.560898627871157	-3.30003451044697	1
-1001000037.F5	-8.66753186618566	-0.647717443904464	0.426824680059196	1.93173799442679	1
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-1001000037.G1	-8.66197051396838	0.490186710294173	2.25922975839205	0.469553217501183	1
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-1001000037.B6	-8.59898549616971	-0.903284024597804	1.02715033802462	1.61831700262053	1
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-1001000037.C9	-7.44540943124005	1.00982301243731	-0.0163850315154234	1.11677603564505	1
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+1001000173.B9	14.09178	-5.353869	3.546184	1.296911	3
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+1001000185.G12	16.255171	-3.382518	3.123406	2.597777	3
+1001000183.C2	16.432063	-3.951484	5.508991	0.602814	3
+1001000173.E1	16.460809	-2.89037	5.201136	2.335582	3
Binary file test-data/hcpc-2.labels.pdf has changed
--- a/test-data/hcpc-3.coord.tab	Thu Jun 27 06:17:08 2019 -0400
+++ b/test-data/hcpc-3.coord.tab	Thu Jul 11 12:31:28 2019 -0400
@@ -1,1034 +1,1034 @@
 Cells	DIM1	DIM2	DIM3	DIM4	Cluster
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Binary file test-data/hcpc-3.labels.pdf has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hcpc.clusters.tab	Thu Jul 11 12:31:28 2019 -0400
@@ -0,0 +1,1034 @@
+Cell	Cluster
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hcpc.factor.extval.txt	Thu Jul 11 12:31:28 2019 -0400
@@ -0,0 +1,20 @@
+ 
+---------------------------------------- 
+purity                         : 0.515 
+entropy                        : 0.459 
+normalized mutual information  : 0.2573 
+variation of information       : 2.7326 
+normalized var. of information : 0.8523 
+---------------------------------------- 
+specificity                    : 0.709 
+sensitivity                    : 0.5529 
+precision                      : 0.368 
+recall                         : 0.5529 
+F-measure                      : 0.4419 
+---------------------------------------- 
+accuracy OR rand-index         : 0.6724 
+adjusted-rand-index            : 0.2231 
+jaccard-index                  : 0.2836 
+fowlkes-mallows-index          : 0.4511 
+mirkin-metric                  : 349208 
+---------------------------------------- 
Binary file test-data/hcpc.labels.pdf has changed
Binary file test-data/hcpc.nolabels.factor.pdf has changed
Binary file test-data/hcpc.nolabels.pdf has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/numeric_factor.tsv	Thu Jul 11 12:31:28 2019 -0400
@@ -0,0 +1,1034 @@
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Binary file test-data/pca.2vs3.pdf has changed
Binary file test-data/pca.coord.pdf has changed
--- a/test-data/pca.coord.tab	Thu Jun 27 06:17:08 2019 -0400
+++ b/test-data/pca.coord.tab	Thu Jul 11 12:31:28 2019 -0400
@@ -1,1034 +1,1034 @@
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Binary file test-data/pca.nolabels.2-lev-factor.pdf has changed
Binary file test-data/pca.nolabels.factors.pdf has changed
Binary file test-data/pca.nolabels.numerical-factor.pdf has changed
Binary file test-data/pca.nolabels.pdf has changed
--- a/test-data/tsne-2.coord.tab	Thu Jun 27 06:17:08 2019 -0400
+++ b/test-data/tsne-2.coord.tab	Thu Jul 11 12:31:28 2019 -0400
@@ -1,1034 +1,1034 @@
 Cells	DIM1	DIM2	DIM3
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