Mercurial > repos > artbio > gsc_high_dimensions_visualisation
changeset 0:cad0001b9cfb draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
| author | artbio |
|---|---|
| date | Mon, 24 Jun 2019 13:39:11 -0400 |
| parents | |
| children | c756ab726a85 |
| files | high_dim_visu.R high_dim_visu.xml test-data/cpm_input.tsv test-data/factor.tsv 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.labels.pdf test-data/hcpc.nolabels.factor.pdf test-data/hcpc.nolabels.pdf test-data/pca.coord.pdf test-data/pca.coord.tab test-data/pca.labels.pdf test-data/pca.nolabels.factors.pdf test-data/pca.nolabels.pdf test-data/shuffled_factor.tsv 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 | 22 files changed, 7503 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/high_dim_visu.R Mon Jun 24 13:39:11 2019 -0400 @@ -0,0 +1,421 @@ +# load packages that are provided in the conda env +options( show.error.messages=F, + error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) +loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") +requiredPackages = c('optparse', 'Rtsne', 'ggplot2', 'ggfortify') +warnings() +library(optparse) +library(FactoMineR) +library(factoextra) +library(Rtsne) +library(ggplot2) +library(ggfortify) +library(RColorBrewer) + + +# Arguments +option_list = list( + make_option( + "--data", + default = NA, + type = 'character', + help = "Input file that contains expression value to visualise" + ), + make_option( + "--sep", + default = '\t', + type = 'character', + help = "File separator [default : '%default' ]" + ), + make_option( + "--colnames", + default = TRUE, + type = 'logical', + help = "Consider first line as header ? [default : '%default' ]" + ), + make_option( + "--out", + default = "res.tab", + type = 'character', + help = "Output name [default : '%default' ]" + ), + make_option( + "--labels", + default = FALSE, + type = 'logical', + help = "add labels in scatter plots [default : '%default' ]" + ), + make_option( + "--factor", + default = '', + type = 'character', + help = "A two column table that specifies factor levels for contrasting data [default : '%default' ]" + ), + make_option( + "--visu_choice", + default = 'PCA', + type = 'character', + help = "visualisation method ('PCA', 'tSNE', 'HCPC') [default : '%default' ]" + ), + make_option( + "--table_coordinates", + default = '', + type = 'character', + help = "Table with plot coordinates [default : '%default' ]" + ), + make_option( + "--Rtsne_seed", + default = 42, + type = 'integer', + help = "Seed value for reproducibility [default : '%default' ]" + ), + make_option( + "--Rtsne_dims", + default = 2, + type = 'integer', + help = "Output dimensionality [default : '%default' ]" + ), + make_option( + "--Rtsne_initial_dims", + default = 50, + type = 'integer', + help = "The number of dimensions that should be retained in the initial PCA step [default : '%default' ]" + ), + make_option( + "--Rtsne_perplexity", + default = 5.0, + type = 'numeric', + help = "perplexity [default : '%default' ]" + ), + make_option( + "--Rtsne_theta", + 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, + type = 'logical', + help = "Whether an initial PCA step should be performed [default : '%default' ]" + ), + make_option( + "--Rtsne_pca_center", + default = TRUE, + type = 'logical', + help = "Should data be centered before pca is applied? [default : '%default' ]" + ), + make_option( + "--Rtsne_pca_scale", + default = FALSE, + type = 'logical', + help = "Should data be scaled before pca is applied? [default : '%default' ]" + ), + make_option( + "--Rtsne_normalize", + default = TRUE, + type = 'logical', + help = "Should data be normalized internally prior to distance calculations? [default : '%default' ]" + ), + make_option( + "--Rtsne_exaggeration_factor", + 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( + "--HCPC_ncluster", + default = -1, + type = 'numeric', + help = "nb.clust, number of clusters to consider in the hierarchical clustering. [default : -1 let HCPC to optimize the number]" + ), + make_option( + "--HCPC_npc", + default = 5, + type = 'integer', + help = "npc, number of dimensions which are kept for HCPC analysis [default : '%default' ]" + ), + make_option( + "--HCPC_metric", + default = 'euclidian', + type = 'character', + help = "Metric to be used for calculating dissimilarities between observations, available 'euclidian' or 'manhattan' [default : '%default' ]" + ), + make_option( + "--HCPC_method", + default = 'ward', + type = 'character', + help = "Clustering method between 'ward','average','single', 'complete', 'weighted' [default :'%default']" + ), + make_option( + "--pdf_out", + default = "out.pdf", + type = 'character', + help = "pdf of plots [default : '%default' ]" + ), + make_option( + "--HCPC_consol", + default = 'TRUE', + type = 'logical', + help = "If TRUE, a k-means consolidation is performed [default :'%default']" + ), + make_option( + "--HCPC_itermax", + default = '10', + type = 'integer', + help = "The maximum number of iterations for the consolidation [default :'%default']" + ), + make_option( + "--HCPC_min", + default = '3', + type = 'integer', + help = "The least possible number of clusters suggested [default :'%default']" + ), + make_option( + "--HCPC_max", + default = -1, + type = 'integer', + help = "The higher possible number of clusters suggested [default :'%default']" + ), + make_option( + "--HCPC_clusterCA", + default = 'rows', + type = 'character', + help = "A string equals to 'rows' or 'columns' for the clustering of Correspondence Analysis results [default :'%default']" + ), + make_option( + "--HCPC_kk", + default = -1, + type = 'numeric', + help = "The maximum number of iterations for the consolidation [default :'%default']" + ) +) + +opt = parse_args(OptionParser(option_list = option_list), + args = commandArgs(trailingOnly = TRUE)) + +if (opt$sep == "tab") {opt$sep <- "\t"} +if (opt$sep == "comma") {opt$sep <- ","} +if(opt$HCPC_max == -1) {opt$HCPC_max <- NULL} +if(opt$HCPC_kk == -1) {opt$HCPC_kk <- Inf} + +data = read.table( + opt$data, + check.names = FALSE, + header = opt$colnames, + row.names = 1, + sep = opt$sep +) + +# Contrasting factor and its colors +if (opt$factor != '') { + contrasting_factor <- read.delim( + opt$factor, + header = TRUE + ) + rownames(contrasting_factor) <- contrasting_factor[,1] + contrasting_factor <- contrasting_factor[colnames(data),] + colnames(contrasting_factor) <- c("id","factor") + contrasting_factor$factor <- as.factor(contrasting_factor$factor) + factorColors <- + with(contrasting_factor, + data.frame(factor = levels(factor), + data.frame(factor = levels(factor), + color = I(brewer.pal(nlevels(factor), name = 'Paired')))) + ) + factor_cols <- factorColors$color[match(contrasting_factor$factor, + factorColors$factor)] +} else { + factor_cols <- rep("deepskyblue4", length(rownames(data))) +} + +################ t-SNE #################### +if (opt$visu_choice == 'tSNE') { + # filter and transpose df for tsne and pca + tdf = t(data) + # make tsne and plot results + set.seed(opt$Rtsne_seed) ## Sets seed for reproducibility + + tsne_out <- Rtsne(tdf, + dims = opt$Rtsne_dims, + initial_dims = opt$Rtsne_initial_dims, + perplexity = opt$Rtsne_perplexity , + theta = opt$Rtsne_theta, + max_iter = opt$Rtsne_max_iter, + pca = opt$Rtsne_pca, + pca_center = opt$Rtsne_pca_center, + pca_scale = opt$Rtsne_pca_scale, + normalize = opt$Rtsne_normalize, + exaggeration_factor=opt$Rtsne_exaggeration_factor) + + embedding <- as.data.frame(tsne_out$Y[,1:2]) + embedding$Class <- as.factor(rownames(tdf)) + gg_legend = theme(legend.position="right") + if (opt$factor == '') { + ggplot(embedding, aes(x=V1, y=V2)) + + geom_point(size=1, color='deepskyblue4') + + gg_legend + + xlab("") + + ylab("") + + ggtitle('t-SNE') + + if (opt$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) + ggplot(embedding, aes(x=V1, y=V2, color=factor)) + + geom_point(size=1) + #, color=factor_cols + gg_legend + + xlab("") + + ylab("") + + ggtitle('t-SNE') + + if (opt$labels) { + geom_text(aes(label=Class, colour=factor),hjust=-0.2, vjust=-0.5, size=1.5) + } + } + ggsave(file=opt$pdf_out, device="pdf") + + #save coordinates table + if(opt$table_coordinates != ''){ + coord_table <- cbind(rownames(tdf),as.data.frame(tsne_out$Y)) + colnames(coord_table)=c("Cells",paste0("DIM",(1:opt$Rtsne_dims))) + } +} + + +######### make PCA with FactoMineR ################# +if (opt$visu_choice == 'PCA') { + pca <- PCA(t(data), ncp=opt$PCA_npc, graph=FALSE) + pdf(opt$pdf_out) + if (opt$labels == FALSE) { + plot(pca, label="none" , col.ind = factor_cols) + } else { + plot(pca, cex=0.2 , col.ind = factor_cols) + } +if (opt$factor != '') { + legend(x = 'topright', + legend = as.character(factorColors$factor), + col = factorColors$color, pch = 16, bty = 'n', xjust = 1, cex=0.7) +} +dev.off() + + #save coordinates table + if(opt$table_coordinates != ''){ + coord_table <- cbind(rownames(pca$ind$coord),as.data.frame(pca$ind$coord)) + colnames(coord_table)=c("Cells",paste0("DIM",(1:opt$PCA_npc))) + } + +} + +########### make HCPC with FactoMineR ########## +if (opt$visu_choice == 'HCPC') { + +# HCPC starts with a PCA +pca <- PCA( + t(data), + ncp = opt$HCPC_npc, + graph = FALSE, + scale.unit = FALSE +) + +PCA_IndCoord = as.data.frame(pca$ind$coord) # coordinates of observations in PCA + +# Hierarchical Clustering On Principal Components Followed By Kmean Clustering +res.hcpc <- HCPC(pca, + nb.clust=opt$HCPC_ncluster, metric=opt$HCPC_metric, method=opt$HCPC_method, + graph=F,consol=opt$HCPC_consol,iter.max=opt$HCPC_itermax,min=opt$HCPC_min,max=opt$HCPC_max, + cluster.CA=opt$HCPC_clusterCA,kk=opt$HCPC_kk) +# HCPC plots +dims <- head(as.data.frame(res.hcpc$call$t$res$eig),2) # dims variances in column 2 +pdf(opt$pdf_out) +plot(res.hcpc, choice="tree") +plot(res.hcpc, choice="bar") +plot(res.hcpc, choice="3D.map") +if (opt$labels == FALSE) { +plot(res.hcpc, choice="map", label="none") +} else { +plot(res.hcpc, choice="map") +} + +# user contrasts on the pca +if (opt$factor != '') { + plot(pca, label="none", habillage="ind", col.hab=factor_cols) + legend(x = 'topright', + legend = as.character(factorColors$factor), + col = factorColors$color, pch = 16, bty = 'n', xjust = 1, cex=0.7) + } +## Clusters to which individual observations belong # used ? +# Clust <- data.frame(Cluster = res.hcpc$data.clust[, (nrow(data) + 1)], +# Observation = rownames(res.hcpc$data.clust)) +# metadata <- data.frame(Observation=colnames(data), row.names=colnames(data)) +# metadata = merge(y = metadata, +# x = Clust, +# by = "Observation") + +# unclear utility +# ObsNumberPerCluster = as.data.frame(table(metadata$Cluster)) +# colnames(ObsNumberPerCluster) = c("Cluster", "ObsNumber") +# +# ## Silhouette Plot # not used +# hc.cut = hcut(PCA_IndCoord, +# k = nlevels(metadata$Cluster), +# hc_method = "ward.D2") +# +# 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)) + colnames(coord_table)=c("Cells",paste0("DIM",(1:opt$HCPC_npc)),"Cluster") + } +} + +## Return coordinates file to user + +if(opt$table_coordinates != ''){ + write.table( + coord_table, + file = opt$table_coordinates, + sep = "\t", + quote = F, + col.names = T, + row.names = F + ) +} + + + + + + + + + + + + + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/high_dim_visu.xml Mon Jun 24 13:39:11 2019 -0400 @@ -0,0 +1,376 @@ +<tool id="high_dimensions_visualisation" name="Generate PCA, tSNE and HCPC" version="0.9.0"> + <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> + </requirements> + <stdio> + <exit_code range="1:" level="fatal" description="Tool exception" /> + </stdio> + <command detect_errors="exit_code"><![CDATA[ + Rscript $__tool_directory__/high_dim_visu.R + --data '$input' + --sep '$input_sep' + --colnames '$input_header' + #if $factor_condition.factor_choice == 'Yes' + --factor '$factor_condition.factor' + #end if + #if $labels == "yes": + --labels 'TRUE' + #else + --labels 'FALSE' + #end if + #if $coord == "yes": + --table_coordinates '$table_coordinates' + #end if + --visu_choice '$visualisation.visu_choice' + #if $visualisation.visu_choice == "tSNE": + --Rtsne_seed '$visualisation.Rtsne_seed' + --Rtsne_perplexity '$visualisation.Rtsne_perplexity' + --Rtsne_theta '$visualisation.Rtsne_theta' + --Rtsne_max_iter '$visualisation.Rtsne_max_iter' + --Rtsne_dims '$visualisation.Rtsne_dims' + --Rtsne_initial_dims '$visualisation.Rtsne_initial_dims' + --Rtsne_pca '$visualisation.Rtsne_pca' + --Rtsne_pca_center '$visualisation.Rtsne_pca_center' + --Rtsne_pca_scale '$visualisation.Rtsne_pca_scale' + --Rtsne_normalize '$visualisation.Rtsne_normalize' + --Rtsne_exaggeration_factor '$visualisation.Rtsne_exaggeration_factor' + #end if + + #if $visualisation.visu_choice == "HCPC": + --HCPC_ncluster '$visualisation.HCPC_ncluster' + --HCPC_npc '$visualisation.HCPC_npc' + --HCPC_metric '$visualisation.HCPC_metric' + --HCPC_method '$visualisation.HCPC_method' + --HCPC_consol '$visualisation.HCPC_consol' + --HCPC_itermax '$visualisation.HCPC_itermax' + --HCPC_min '$visualisation.HCPC_min' + --HCPC_max '$visualisation.HCPC_max' + --HCPC_clusterCA '$visualisation.HCPC_clusterCA' + --HCPC_kk '$visualisation.HCPC_kk' + #end if + + #if $visualisation.visu_choice == "PCA": + --PCA_npc '$visualisation.PCA_npc' + #end if + + + --pdf_out '$pdf_out' + +]]></command> + <inputs> + <param name="input" type="data" format="txt,tabular" label="expression data"/> + <param name="input_sep" type="select" label="Input column separator"> + <option value="tab" selected="true">Tabs</option> + <option value=",">Comma</option> + </param> + <param name="input_header" type="select" label="Consider first line of input file as header?"> + <option value="TRUE" selected="true">Yes</option> + <option value="FALSE">No</option> + </param> + <param name="labels" type="select" label="Add sample labels to scatter plot" > + <option value="no" selected="true">No Labels</option> + <option value="yes" >Label points</option> + </param> + <conditional name="factor_condition"> + <param label="Do you wish to contrast cells with a factor" name="factor_choice" type="select"> + <option value="Yes">Yes</option> + <option value="No" selected="true">No</option> + </param> + <when value="Yes"> + <param name="factor" type="data" format="tabular" label="Factor to constrast data" + help="A two-column data frame, first column contains data labels, second column contains the levels of a factor to contrast visualisation" /> + </when> + <when value="No"> + </when> + </conditional> + <conditional name="visualisation"> + <param label="Choose visualisation method" name="visu_choice" type="select"> + <option value="PCA" selected="True">PCA</option> + <option value="HCPC">HCPC</option> + <option value="tSNE">t-SNE</option> + </param> + <when value="tSNE"> + <param name="Rtsne_seed" value="42" type="integer" label="Seed value for reproducibility of t-SNE" help="Set to 42 as default" /> + <param name="Rtsne_dims" value="2" type="integer" label="dims (t-SNE)" help="Output dimensionality (should not be greater than 3)" /> + <param name="Rtsne_pca" type="select" label="pca (t-SNE)" help="Whether an initial PCA step should be performed" > + <option value="TRUE" selected="true">Yes</option> + <option value="FALSE">False</option> + </param> + <param name="Rtsne_initial_dims" value="50" type="integer" label="initial dims (t-SNE)" help="The number of dimensions that should be retained in the initial PCA step" /> + <param name="Rtsne_pca_center" type="select" label="Centering data" help="Should data be centered before pca is applied? " > + <option value="TRUE" selected="true">Yes</option> + <option value="FALSE">False</option> + </param> + <param name="Rtsne_pca_scale" type="select" label="Scalling data" help="Should data be scaled before pca is applied? " > + <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> + <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)"/> + <param name="Rtsne_exaggeration_factor" value="12.0" type="float" label="Exageration factor" help="Exaggeration factor used to multiply the P matrix in the first part of the optimization" /> + <param name="Rtsne_max_iter" value="1000" type="integer" label="Number of iterations (default: 1000)" + help="The number of iterations that Rtsne executes to improve low dim representation (gradient descent optimization)" /> + </when> + <when value="HCPC"> + <param name="HCPC_npc" value="5" type="integer" label="Number of principal components to keep" + help="The number of dimensions which are kept for HCPC analysis (default=5)" /> + <param name="HCPC_ncluster" value="-1" type="integer" label="Number of clusters in Hierar. Clustering" + help="nb.clust, the number of clusters to consider in the hierarchical clustering. (default : -1, let HCPC to optimize the number)" /> + <param name="HCPC_metric" type="select" label="Dissimilarity metric" help="Metric to be used for calculating dissimilarities between observations, available 'euclidian' or 'manhattan'? " > + <option value="euclidian" selected="true">euclidian</option> + <option value="manhattan">manhattan</option> + </param> + <param name="HCPC_method" type="select" label="Clustering method" help="Clustering method between 'ward', 'average', 'single', 'complete', 'weighted' " > + <option value="ward" selected="true">ward</option> + <option value="average">average</option> + <option value="single">single</option> + <option value="complete">complete</option> + <option value="weighted">weighted</option> + </param> + <param name="HCPC_consol" type="select" label="k-means consolidation" help="If TRUE, a k-means consolidation is performed" > + <option value="TRUE" selected="true">Yes</option> + <option value="FALSE">False</option> + </param> + <param name="HCPC_itermax" value="10" type="integer" label="Maximum number of iterations for consolidation" + help=" (default=10)" /> + <param name="HCPC_min" value="3" type="integer" label="min number of clusters" + help=" The least possible number of clusters suggested (default=3)" /> + <param name="HCPC_max" value="-1" type="text" label="max number of clusters" + help=" The higher possible number of clusters suggested, by default the minimum between 10 and the number of individuals divided by 2. (default=-1)" /> + <param name="HCPC_clusterCA" type="select" label="clusterCA, Clustering against rows or columns" help="default(rows)" > + <option value="rows" selected="true">Rows</option> + <option value="cols">Columns</option> + </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)" /> + </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)" /> + </when> + </conditional> + <param label="Return scatter plot table coordinates" name="coord" type="select"> + <option value="no" selected="True">No</option> + <option value="yes">Yes</option> + </param> + + </inputs> + <outputs> + <data name="pdf_out" format="pdf" label="${visualisation.visu_choice} on ${on_string}" /> + <data name="table_coordinates" format="tabular" label="Scatter plot coordinates from ${tool.name} on ${on_string}" > + <filter>coord == 'yes'</filter> + </data> + </outputs> + <tests> + <!-- test PCA --> + <test> + <param name="input" value="cpm_input.tsv" ftype="txt"/> + <param name="labels" value="yes" /> + <param name="visu_choice" value="PCA" /> + <param name="factor_choice" value="No" /> + <output name="pdf_out" file="pca.labels.pdf" ftype="pdf"/> + </test> + <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" /> + <output name="pdf_out" file="pca.nolabels.pdf" ftype="pdf"/> + </test> + <!-- test Coordinates tables 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="coord" value="yes" /> + <param name="factor_choice" value="No" /> + <output name="pdf_out" file="pca.nolabels.pdf" ftype="pdf"/> + <output name="table_coordinates" file="pca.coord.tab" ftype="tabular"/> + </test> + <!-- test 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="factor.tsv" ftype="txt"/> + <output name="pdf_out" file="pca.nolabels.factors.pdf" ftype="pdf"/> + </test> + <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="shuffled_factor.tsv" ftype="txt"/> + <output name="pdf_out" file="pca.nolabels.factors.pdf" ftype="pdf"/> + </test> + <!-- test HCPC --> + <test> + <param name="input" value="cpm_input.tsv" ftype="txt"/> + <param name="labels" value="yes" /> + <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"/> + </test> + <!-- test factor contrasting on HCPC --> + <test> + <param name="input" value="cpm_input.tsv" ftype="txt"/> + <param name="labels" value="no" /> + <param name="visu_choice" value="HCPC" /> + <param name="HCPC_npc" value="5"/> + <param name="HCPC_ncluster" value="-1"/> + <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"/> + </test> + <test> + <param name="input" value="cpm_input.tsv" ftype="txt"/> + <param name="labels" value="no" /> + <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"/> + </test> + <test> + <param name="input" value="cpm_input.tsv" ftype="txt"/> + <param name="labels" value="yes" /> + <param name="visu_choice" value="HCPC" /> + <param name="coord" value="yes" /> + <param name="HCPC_method" value="average"/> + <param name="HCPC_metric" value="manhattan"/> + <param name="HCPC_npc" value="4" /> + <output name="pdf_out" file="hcpc-2.labels.pdf" ftype="pdf"/> + <output name="table_coordinates" file="hcpc-2.coord.tab" ftype="tabular"/> + </test> + <test> + <param name="input" value="cpm_input.tsv" ftype="txt"/> + <param name="labels" value="yes" /> + <param name="visu_choice" value="HCPC" /> + <param name="coord" value="yes" /> + <param name="HCPC_method" value="single"/> + <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="table_coordinates" file="hcpc-3.coord.tab" ftype="tabular"/> + </test> + <!-- test t-SNE --> + <test> + <param name="input" value="cpm_input.tsv" ftype="txt"/> + <param name="labels" value="yes" /> + <param name="visu_choice" value="tSNE" /> + <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"/> + </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="Rtsne_perplexity" value="10"/> + <param name="Rtsne_theta" value="1" /> + <output name="pdf_out" file="tsne.nolabels.pdf" ftype="pdf"/> + </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> + <param name="input" value="cpm_input.tsv" ftype="txt"/> + <param name="labels" value="yes" /> + <param name="visu_choice" value="tSNE" /> + <param name="factor_choice" value="Yes" /> + <param name="factor" value="shuffled_factor.tsv" ftype="txt"/> + <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"/> + </test> + </tests> + <help> + +**What it does** + +Takes as an input a matrix of n observations (columns, generally n RNAseq library) of k variables +(rows, generally k genes). + +k variables define a space of k dimensions. Any observation +of k expression values for k genes (the purpose of one RNAseq experiment) can be assigned +to a position in the k-dim space, of coordinates c1, c2, c3, ..., ck. + +Since visualisation in more than 3 dimensions is not easy for a human beeing, there is +a number of methods to "reduce" or "project" a k-dim space in a space of 2 or 3 dimensions. +This is of great help, not only to summarise the data, but also to find similarities, common trends +between the data (under the hypothesis that similar data are closer in the k-dimension space). + +This tool returns the visualisation of a dimensional reduction using either: + +* Principal Components Analysis (PCA) +* Hierarchical Clustering of Principal Components (HCPC) +* t-distributed Stochastic Neighbor Embedding + +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. + +** 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 +table. It may also contain more identifiers than those provided in the data table. + + </help> + <citations> + <citation type="bibtex">@Article{, + title = {Visualizing High-Dimensional Data Using t-SNE}, + volume = {9}, + pages = {2579-2605}, + year = {2008}, + author = {L.J.P. {van der Maaten} and G.E. Hinton}, + journal = {Journal of Machine Learning Research}, + } + </citation> + <citation type="bibtex">@Article{, + title = {Accelerating t-SNE using Tree-Based Algorithms}, + volume = {15}, + pages = {3221-3245}, + year = {2014}, + author = {L.J.P. {van der Maaten}}, + journal = {Journal of Machine Learning Research}, + } + </citation> + <citation type="bibtex">@Manual{, + title = {{Rtsne}: T-Distributed Stochastic Neighbor Embedding using + Barnes-Hut Implementation}, + author = {Jesse H. Krijthe}, + year = {2015}, + note = {R package version 0.15}, + url = {https://github.com/jkrijthe/Rtsne}, + } + </citation> + </citations> +</tool>
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8.39719728254004 5.04161734471325 -21.6460892550815 2 +1001000260.B9 11.702000998555 8.89721487820175 20.5093834003081 -13.9499520223311 2 +1001000175.C8 11.8245588767586 1.43415791116304 -9.89325596505814 5.22478111585988 2 +1001000180.A11 11.8620598382406 10.7408402404226 -2.30832521854882 1.90389162959351 2 +1001000173.H9 11.9274838375695 -14.5075730557321 15.9058602273517 2.86555660029062 3 +1001000183.E12 11.9968706457248 15.0635878619859 -9.44141493572951 14.1967506144241 2 +1001000260.A2 11.9975856509856 5.49922432500082 8.91638539457685 -11.5489281832518 2 +1001000245.D8 12.0405819284768 -1.79264392816416 -9.05137027480564 -13.6309242243651 2 +1001000259.D2 12.1000446481206 13.8695448065545 2.21456084484126 -22.127084867631 2 +1001000254.C2 12.1654722254838 13.8110948261196 -3.68618348221329 5.94738490330634 2 +1001000182.G12 12.1722738514459 7.75007603794407 -14.1725073601633 6.10161824178585 2 +1001000258.G9 12.2630301482599 11.595964263995 9.4458434885055 -9.25014665733725 2 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15.3231446913216 10.449010991627 20.6056839797693 -9.54012080317468 2 +1001000182.B3 15.348883886341 -16.7113084564123 3.64121023017951 -1.73054285447509 3 +1001000250.B2 15.3535677239615 18.184410350891 -5.43079789438798 -5.62552712538286 2 +1001000183.B10 15.4495835252986 9.70206492238497 -13.540541978713 7.3526732751627 2 +1001000260.A4 15.454668844527 9.37573798529454 13.3029729322362 -16.1028544876014 2 +1001000175.B4 15.4888020603207 -15.7128164684088 -0.572075992783389 -6.62596060156 3 +1001000185.G2 15.5325801222606 2.97050726792772 -9.1169052924884 1.62791214866776 2 +1001000175.F6 15.5550573245267 9.37179518529324 -8.47576911727428 11.3926451553317 2 +1001000268.G2 15.5744279810026 13.3869123699126 4.66546009749829 -18.0038185907013 2 +1001000174.A9 15.7639476628219 -20.8027957910005 8.26635202133912 1.70821730711849 3 +1001000182.C7 15.8068502414116 -0.202234840590374 -10.2221177617761 5.72388162057876 2 +1001000268.B2 15.8213810870891 4.18827363762616 12.8383791000367 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8.2304575973186 -2.26804055292328 3 +1001000173.H1 19.5414001223696 2.82719787354895 -10.4267159934119 -1.58088646107355 2 +1001000182.G6 19.6955013793227 -5.7129858086817 -4.34564091806117 5.57012291785285 3 +1001000184.F3 19.7641420319871 -15.8016560799371 4.1337871422009 -1.31509222329625 3 +1001000183.H9 19.8040862798573 2.34026679121815 0.946503575459783 13.782112979075 3 +1001000174.D7 19.8210535318807 13.650291351336 -10.2434313231638 10.5136219648195 2 +1001000175.B1 19.9358825472938 9.96812445326814 -7.42088541250884 3.20579211629786 2 +1001000181.C7 20.0130262565797 16.929030011592 -1.1780155360274 7.76010729849612 2 +1001000184.D12 20.1086111323841 -18.366363019467 0.34691531421176 -6.36174674470735 3 +1001000250.G7 20.2500850790508 -6.04119722214316 -5.37191681752543 -4.57238859868769 3 +1001000183.E11 20.3019053349246 7.57034997907923 -6.29939405797639 5.54659365797868 2 +1001000183.G11 20.3365766779069 10.2166591415965 -14.3237191917432 -3.22426865922061 2 +1001000260.G5 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5.32538577343754 -12.7404128982696 2 +1001000184.C12 23.3071465819817 -6.1264903429666 4.1879380799325 1.38115462635053 3 +1001000182.E10 23.6579243987362 -17.7785288942683 3.25027504575056 -0.728918483159551 3 +1001000183.G10 23.6782192719696 5.0457157624589 -9.52325212203999 10.5686220938712 3 +1001000174.G9 23.7301096333159 -12.3377952846118 -0.504005754505481 -7.26699687328643 3 +1001000173.F9 23.8210538622188 14.0560948246765 14.1631528134328 9.45313711188329 3 +1001000185.B4 23.8404458372487 -16.0940774492058 10.7368295682249 1.43840198471185 3 +1001000183.G8 23.9730975171806 -7.20564100844614 -2.46972948847932 10.3355149309016 3 +1001000174.G5 24.0218457976312 -14.2148502977989 9.18933670915131 -3.03932766990135 3 +1001000175.F11 24.0509698315103 14.2912234302442 1.64539325583901 12.9604744303602 3 +1001000184.F7 24.0823185592621 0.985356152036102 -2.70030141880282 8.05547580382749 3 +1001000185.B12 24.0863619840829 2.33044492284779 0.376493077064887 12.7195282155213 3 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7.06856520537896 -19.1232337182089 3 +1001000184.D3 25.2913704659152 -8.82814086746923 6.25728497427307 7.35289027137063 3 +1001000185.A9 25.3020727614444 -12.0702497618453 -10.2260382389549 0.0666416780399849 3 +1001000183.A4 25.827031071658 6.62297838362202 4.09009682840042 4.02181525747559 3 +1001000184.G11 25.8944502386844 -11.2786389664589 6.39853634984025 10.2645929115951 3 +1001000182.F3 25.9409318691816 -12.6693263083768 -0.552378982919714 -4.39769861222965 3 +1001000183.B5 25.9784856340848 12.87065784094 -4.33296064721053 3.71776076346886 3 +1001000182.A11 26.0386730296089 10.8463917478665 -9.75074496163007 9.22303806493391 3 +1001000184.A1 26.0518602246024 -2.53173771587387 3.06134834008925 12.4609714288876 3 +1001000174.G11 26.1564628806059 6.3052303995335 -0.356379383733954 10.557387902338 3 +1001000175.C7 26.2345508386697 2.5396274752759 -7.77919526997443 8.81459565574125 3 +1001000259.E2 26.2628407956477 16.3632302578545 23.1733131530717 -9.21564053624014 3 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15.3231446913216 10.449010991627 20.6056839797693 -9.54012080317468 2 +1001000182.B3 15.348883886341 -16.7113084564123 3.64121023017951 -1.73054285447509 3 +1001000250.B2 15.3535677239615 18.184410350891 -5.43079789438798 -5.62552712538286 2 +1001000183.B10 15.4495835252986 9.70206492238497 -13.540541978713 7.3526732751627 2 +1001000260.A4 15.454668844527 9.37573798529454 13.3029729322362 -16.1028544876014 2 +1001000175.B4 15.4888020603207 -15.7128164684088 -0.572075992783389 -6.62596060156 3 +1001000185.G2 15.5325801222606 2.97050726792772 -9.1169052924884 1.62791214866776 2 +1001000175.F6 15.5550573245267 9.37179518529324 -8.47576911727428 11.3926451553317 2 +1001000268.G2 15.5744279810026 13.3869123699126 4.66546009749829 -18.0038185907013 2 +1001000174.A9 15.7639476628219 -20.8027957910005 8.26635202133912 1.70821730711849 3 +1001000182.C7 15.8068502414116 -0.202234840590374 -10.2221177617761 5.72388162057876 2 +1001000268.B2 15.8213810870891 4.18827363762616 12.8383791000367 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8.2304575973186 -2.26804055292328 3 +1001000173.H1 19.5414001223696 2.82719787354895 -10.4267159934119 -1.58088646107355 2 +1001000182.G6 19.6955013793227 -5.7129858086817 -4.34564091806117 5.57012291785285 3 +1001000184.F3 19.7641420319871 -15.8016560799371 4.1337871422009 -1.31509222329625 3 +1001000183.H9 19.8040862798573 2.34026679121815 0.946503575459783 13.782112979075 3 +1001000174.D7 19.8210535318807 13.650291351336 -10.2434313231638 10.5136219648195 2 +1001000175.B1 19.9358825472938 9.96812445326814 -7.42088541250884 3.20579211629786 2 +1001000181.C7 20.0130262565797 16.929030011592 -1.1780155360274 7.76010729849612 2 +1001000184.D12 20.1086111323841 -18.366363019467 0.34691531421176 -6.36174674470735 3 +1001000250.G7 20.2500850790508 -6.04119722214316 -5.37191681752543 -4.57238859868769 3 +1001000183.E11 20.3019053349246 7.57034997907923 -6.29939405797639 5.54659365797868 3 +1001000183.G11 20.3365766779069 10.2166591415965 -14.3237191917432 -3.22426865922061 2 +1001000260.G5 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5.32538577343754 -12.7404128982696 2 +1001000184.C12 23.3071465819817 -6.1264903429666 4.1879380799325 1.38115462635053 3 +1001000182.E10 23.6579243987362 -17.7785288942683 3.25027504575056 -0.728918483159551 3 +1001000183.G10 23.6782192719696 5.0457157624589 -9.52325212203999 10.5686220938712 3 +1001000174.G9 23.7301096333159 -12.3377952846118 -0.504005754505481 -7.26699687328643 3 +1001000173.F9 23.8210538622188 14.0560948246765 14.1631528134328 9.45313711188329 3 +1001000185.B4 23.8404458372487 -16.0940774492058 10.7368295682249 1.43840198471185 3 +1001000183.G8 23.9730975171806 -7.20564100844614 -2.46972948847932 10.3355149309016 3 +1001000174.G5 24.0218457976312 -14.2148502977989 9.18933670915131 -3.03932766990135 3 +1001000175.F11 24.0509698315103 14.2912234302442 1.64539325583901 12.9604744303602 3 +1001000184.F7 24.0823185592621 0.985356152036102 -2.70030141880282 8.05547580382749 3 +1001000185.B12 24.0863619840829 2.33044492284779 0.376493077064887 12.7195282155213 3 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7.06856520537896 -19.1232337182089 3 +1001000184.D3 25.2913704659152 -8.82814086746923 6.25728497427307 7.35289027137063 3 +1001000185.A9 25.3020727614444 -12.0702497618453 -10.2260382389549 0.0666416780399849 3 +1001000183.A4 25.827031071658 6.62297838362202 4.09009682840042 4.02181525747559 3 +1001000184.G11 25.8944502386844 -11.2786389664589 6.39853634984025 10.2645929115951 3 +1001000182.F3 25.9409318691816 -12.6693263083768 -0.552378982919714 -4.39769861222965 3 +1001000183.B5 25.9784856340848 12.87065784094 -4.33296064721053 3.71776076346886 3 +1001000182.A11 26.0386730296089 10.8463917478665 -9.75074496163007 9.22303806493391 3 +1001000184.A1 26.0518602246024 -2.53173771587387 3.06134834008925 12.4609714288876 3 +1001000174.G11 26.1564628806059 6.3052303995335 -0.356379383733954 10.557387902338 3 +1001000175.C7 26.2345508386697 2.5396274752759 -7.77919526997443 8.81459565574125 3 +1001000259.E2 26.2628407956477 16.3632302578545 23.1733131530717 -9.21564053624014 3 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pca.coord.tab Mon Jun 24 13:39:11 2019 -0400 @@ -0,0 +1,1034 @@ +Cells DIM1 DIM2 DIM3 DIM4 DIM5 +1001000173.G8 -5.31693701953163 -3.46194654365546 1.74316013071281 -3.83334321406266 -0.425688901476677 +1001000173.B4 10.0361145342526 -6.4001376231127 1.82042981334608 -2.10784366673874 0.613700200499314 +1001000173.A2 3.79246289405376 2.13924734561231 -1.76540854841281 3.94878676664593 -0.308618844431403 +1001000173.E2 -4.32884658571041 0.402848740812616 -3.44065122508972 -0.93706795519332 -0.939747754792572 +1001000173.F6 -1.57651890662075 0.365062762744466 -3.33929898056208 -0.114850347546217 -1.11602793358278 +1001000173.B12 9.70073898225409 -6.03006818252483 5.28179285855865 0.167774846420523 0.56098251541239 +1001000173.H1 5.89792373696629 0.770986928316156 -3.40404737253666 -0.578943784171644 1.16374825389916 +1001000173.E4 -1.98714053195272 -3.915954034033 2.61563019157785 -1.01526684041459 0.581308989720759 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/shuffled_factor.tsv Mon Jun 24 13:39:11 2019 -0400 @@ -0,0 +1,1034 @@ +id factor +1001000259.F11 d +1001000037.C10 c +1001000175.E10 a +1001000012.H7 c +1001000260.B11 d +1001000180.D11 a +1001000173.G6 a +1001000182.C7 b +1001000183.C5 b +1001000031.H7 c +1001000245.B10 d +1001000173.H4 a +1001000175.C6 a +1001000182.F2 b +1001000250.G1 d +1001000037.E7 c +1001000174.D4 a +1001000230.D3 d +1001000174.A1 a +1001000174.H6 a +1001000183.F5 b +1001000184.F6 b +1001000185.C2 b +1001000184.B8 b +1001000184.A11 b +1001000173.D2 a +1001000175.E12 a +1001000174.A8 a +1001000231.C10 d +1001000268.H4 e +1001000174.C6 a +1001000250.G2 d +1001000173.B11 a +1001000268.C3 e +1001000183.C2 b +1001000174.E3 a +1001000182.G3 b +1001000259.G11 d +1001000175.F9 a +1001000185.D3 b +1001000184.B7 b +1001000037.C4 c +1001000260.F2 d +1001000185.E6 b +1001000031.G12 c +1001000180.B3 a +1001000250.E2 d +1001000250.A2 d +1001000184.A7 b 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