# HG changeset patch # User artbio # Date 1567413560 14400 # Node ID 569334568afafc90b696ff41932603cd98ed5ca0 # Parent 8e17c31c536a27dd72c916e17eeddf107faa291e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1b98c85982a2a9f9df4b318f672b9b68cff66a93" diff -r 8e17c31c536a -r 569334568afa high_dim_visu.R --- a/high_dim_visu.R Thu Jul 11 12:31:28 2019 -0400 +++ b/high_dim_visu.R Mon Sep 02 04:39:20 2019 -0400 @@ -2,7 +2,6 @@ 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) @@ -12,6 +11,7 @@ library(ggfortify) library(RColorBrewer) library(ClusterR) +library(data.table) # Arguments option_list = list( @@ -161,9 +161,9 @@ ), make_option( "--HCPC_metric", - default = 'euclidian', + default = 'euclidean', type = 'character', - help = "Metric to be used for calculating dissimilarities between observations, available 'euclidian' or 'manhattan' [default : '%default' ]" + help = "Metric to be used for calculating dissimilarities between observations, available 'euclidean' or 'manhattan' [default : '%default' ]" ), make_option( "--HCPC_method", @@ -209,7 +209,7 @@ ), make_option( "--HCPC_kk", - default = -1, + default = Inf, type = 'numeric', help = "The maximum number of iterations for the consolidation [default :'%default']" ), @@ -220,10 +220,16 @@ help = "Output result of HCPC clustering : two column table (cell identifiers and clusters) [default :'%default']" ), make_option( - "--mutual_info", + "--HCPC_mutual_info", default = "", type = "character", help = "Output file of external validation of HCPC clustering with factor levels [default :'%default']" + ), + make_option( + "--HCPC_cluster_description", + default = "", + type = "character", + help = "Output file with variables most contributing to clustering [default :'%default']" ) ) @@ -436,7 +442,7 @@ col = factorColors$color, pch = 16, bty = 'n', xjust = 1, cex=0.7) ## Normalized Mutual Information - sink(opt$mutual_info) + sink(opt$HCPC_mutual_info) res <- external_validation( true_labels = as.numeric(contrasting_factor$factor), clusters = as.numeric(res.hcpc$data.clust$clust), @@ -448,6 +454,7 @@ 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$data.clust)) @@ -484,6 +491,31 @@ } +# Description of cluster by most contributing variables / gene expressions + +# first transform list of vectors in a list of dataframes +extract_description <- lapply(res.hcpc$desc.var$quanti, as.data.frame) +# second, transfer rownames (genes) to column in the dataframe, before rbinding +extract_description_w_genes <- Map(cbind, + extract_description, + genes= lapply(extract_description, rownames) + ) +# Then use data.table to collapse all generated dataframe, with the cluster id in first column +# using the {data.table} rbindlist function +cluster_description <- rbindlist(extract_description_w_genes, idcol = "cluster_id") +cluster_description = cluster_description[ ,c(8, 1, 2, 3,4,5,6,7)] # reorganize columns + + +# Finally, output cluster description data frame +write.table( + cluster_description, + file = opt$HCPC_cluster_description, + sep = "\t", + quote = F, + col.names = T, + row.names = F + ) + } ## Return coordinates file to user @@ -509,15 +541,4 @@ col.names = T, row.names = F ) -} - - - - - - - - - - - +} diff -r 8e17c31c536a -r 569334568afa high_dim_visu.xml --- a/high_dim_visu.xml Thu Jul 11 12:31:28 2019 -0400 +++ b/high_dim_visu.xml Mon Sep 02 04:39:20 2019 -0400 @@ -1,4 +1,4 @@ - + from highly dimensional expression data r-optparse @@ -7,6 +7,7 @@ r-rtsne r-ggfortify r-clusterr + @@ -53,6 +54,7 @@ --HCPC_max '$visualisation.HCPC_max' --HCPC_clusterCA '$visualisation.HCPC_clusterCA' --HCPC_kk '$visualisation.HCPC_kk' + --HCPC_cluster_description '$HCPC_cluster_description' #if $visualisation.res_clustering == "yes": --HCPC_clust '$HCPC_clust' #end if @@ -65,7 +67,7 @@ #end if #if $visualisation.visu_choice == "HCPC" and $factor_condition.factor_choice == "Yes": - --mutual_info '$mutual_info' + --HCPC_mutual_info '$HCPC_mutual_info' #end if --pdf_out '$pdf_out' @@ -134,34 +136,43 @@ - - + help="nb.clust - an integer. If 0, the tree is cut at the level the user clicks on (not working in Galaxy). If -1, the tree is + automatically cut at the suggested level (see details). If a (positive) integer, the tree is cut with nb.cluters clusters." /> + + - + - - + + help="An integer. The maximum number of iterations for the consolidation. (default=10)" /> + help="an integer. The least possible number of clusters suggested. (default=3)" /> - + help="The higher possible number of clusters suggested, by default the minimum between 10 and the number of individuals divided by 2. (default=-1)" /> + - + @@ -184,14 +195,18 @@ coord == 'yes' - + visualisation['visu_choice'] == 'HCPC' and factor_condition['factor_choice'] == 'Yes' visualisation['visu_choice'] == 'HCPC' and visualisation['res_clustering'] == 'yes' + + visualisation['visu_choice'] == 'HCPC' + + @@ -271,6 +286,7 @@ + @@ -283,8 +299,9 @@ - + + @@ -293,6 +310,7 @@ + @@ -304,6 +322,7 @@ + @@ -311,11 +330,12 @@ - + + diff -r 8e17c31c536a -r 569334568afa test-data/hcpc.cluster_description.1.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hcpc.cluster_description.1.tab Mon Sep 02 04:39:20 2019 -0400 @@ -0,0 +1,1180 @@ +genes cluster_id v.test Mean in category Overall mean sd in category Overall sd p.value +TUSC3 1 11.8890897711964 2.02149769035256 0.820349274023337 3.81496317321131 2.61166315266037 1.34868362907211e-32 +USMG5 1 8.61018275981449 5.36922025791415 4.36307228245837 3.30870030072204 3.02077642160404 7.29441907532539e-18 +TM4SF1 1 6.8501233340706 2.60299136171499 1.64679530949995 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04:39:20 2019 -0400 @@ -0,0 +1,1231 @@ +genes cluster_id v.test Mean in category Overall mean sd in category Overall sd p.value +TUSC3 1 9.64226245491482 1.58846421413198 0.820349274023337 3.47195156241725 2.61166315266037 5.30066060421869e-22 +USMG5 1 5.75087525581821 4.89295851056519 4.36307228245837 3.37773714868832 3.02077642160404 8.87826071601112e-09 +TM4SF1 1 4.30513402655702 2.12063826557369 1.64679530949995 4.15092195695276 3.60842472917828 1.66884668352345e-05 +WASF3 1 2.3686373498309 2.47567150728554 2.23304493116436 3.69290575886789 3.35822425701289 0.0178537498791563 +RPS6 1 -2.02142946490481 7.57774368453375 7.77324497980439 3.69929873265015 3.1707422903076 0.0432353271268453 +STOX2 1 -2.03230776521167 0.456131537141282 0.575761068032365 1.83974078909003 1.92982896728664 0.0421225088463805 +ZNF815 1 -2.05822775838923 0.168343625205738 0.246326932456439 1.13094339680922 1.24216164846543 0.0395682751672086 +HRASLS 1 -2.18810433400509 0.533092539417367 0.672637228800667 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1.64679530949995 1.86648693610858 3.60842472917828 1.12651355511703e-15 diff -r 8e17c31c536a -r 569334568afa test-data/hcpc.cluster_description.5.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hcpc.cluster_description.5.tab Mon Sep 02 04:39:20 2019 -0400 @@ -0,0 +1,1178 @@ +genes cluster_id v.test Mean in category Overall mean sd in category Overall sd p.value +TUSC3 1 11.9142858023152 2.02648904267441 0.820349274023337 3.81834581414514 2.61166315266037 9.97169617739689e-33 +USMG5 1 8.39755631476141 5.34636759612311 4.36307228245837 3.3204661574193 3.02077642160404 4.55865936650362e-17 +TM4SF1 1 6.88218287090609 2.60941850087972 1.64679530949995 4.48576784413717 3.60842472917828 5.89422778470414e-12 +WASF3 1 3.78804329877795 2.7261473017572 2.23304493116436 3.81852542872013 3.35822425701289 0.00015183839224081 +RPS29 1 3.36197375608184 4.41131394198962 4.10483867741957 2.7351913375762 2.35173643708298 0.000773874782658214 +ATP6V0C 1 2.64343334249021 4.09672975637321 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