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Commit message:
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/plotheatmap commit 7e9d6b283879b45d5fe673767668c06104d31609-dirty |
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added:
plotheatmap.xml script.R test-data/count.matrix test-data/heatmap.pdf test-data/stats.data |
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| diff -r 000000000000 -r bd8fd161908b plotheatmap.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/plotheatmap.xml Wed Jul 12 14:29:51 2017 -0400 |
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| @@ -0,0 +1,87 @@ +<tool id="plotheatmap" name="plotHeatmap" version="1.0"> + <description>Plot heatmap</description> + <requirements> + <requirement type="package" version="1.34.0">bioconductor-preprocesscore</requirement> + <requirement type="package" version="3.0.1">r-gplots</requirement> + </requirements> + <command detect_errors="aggressive"><![CDATA[ +Rscript '$__tool_directory__/script.R' +'$count_matrix' +'$stats_matrix' +$filter.log_fc +$filter.log_cpm +$filter.pvalue +$filter.fdr +$heatmap.cluster_row +$heatmap.cluster_col +$heatmap.hclust_method +$plotparm.col_marg +$plotparm.row_marg +$plotparm.pdf_width +$plotparm.pdf_height + ]]></command> + <inputs> + <param name="count_matrix" type="data" format="tabular" label="Output dataset 'count_matrix' from tool countMatrixForEdger"/> + <param name="stats_matrix" type="data" format="tabular" label="Output dataset 'output' from tool edgeR"/> + <section name="filter" title="Filtering parameters" expanded="true"> + <param name="log_fc" type="float" value="0.5" label="A log FC threshold"/> + <param name="log_cpm" type="float" value="0.5" label="A log CPM threshold"/> + <param name="pvalue" type="float" min="0" max="1" value="0.5" label="A p-value threshold"/> + <param name="fdr" type="float" min="0" max="1" value="0.5" label="An FDR threshold"/> + </section> + <section name="heatmap" title="Heatmap parameters"> + <param name="cluster_row" type="boolean" truevalue="Yes" falsevalue="No" checked="true" label="Determines if the row dendrogram should be reordered"/> + <param name="cluster_col" type="boolean" truevalue="Yes" falsevalue="No" label="Determines if the column dendrogram should be reordered"/> + <param name="hclust_method" type="select" label="Hierarchical clustering method"> + <option value="ward.D">ward.D</option> + <option value="ward.D2">ward.D2</option> + <option value="single">single</option> + <option value="complete">complete</option> + <option value="average" selected="true">average</option> + <option value="mcquitty">mcquitty</option> + <option value="median">median</option> + <option value="centroid">centroid</option> + </param> + </section> + <section name="plotparm" title="Plot parameters"> + <param name="col_marg" type="float" value="7" label="Margins for column names"/> + <param name="row_marg" type="float" value="8" label="Margins for row names"/> + <param name="pdf_width" type="float" value="7" label="Width of the graphics region in inches (pdf width)"/> + <param name="pdf_height" type="float" value="7" label="Height of the graphics region in inches (pdf height)"/> + </section> + </inputs> + <outputs> + <data name="haetamappdf" format="pdf" from_work_dir="heatmap.pdf"/> + </outputs> + <tests> + <test> + <param name="count_matrix" value="count.matrix"/> + <param name="stats_matrix" value="stats.data"/> + <param name="log_fc" value="1"/> + <param name="log_cpm" value="2"/> + <param name="pvalue" value="0.05"/> + <param name="fdr" value="0.1"/> + <output name="haetamappdf" file="heatmap.pdf" ftype="pdf" compare="sim_size"/> + </test> + </tests> + <help><![CDATA[ +**What it does** + +It takes a list of genes based on set filtering criteria and draws them on heatmap. + +**Example** + +The following filtering options: +A log FC threshold = 0.5 +A log CPM threshold = 0.5 +A p-value threshold = 0.05 +An FDR threshold = 0.1 +mean that you select genes whose values in output table from edgeR are: +* absolute value of log FC is greater than or equal to 0.5 +* log CPM is greater than or equal to 0.5 +* p-value is less than or equal to 0.05 +* FDR is less than or equal to 0.1 + ]]></help> + <citations> + </citations> +</tool> |
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| diff -r 000000000000 -r bd8fd161908b script.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/script.R Wed Jul 12 14:29:51 2017 -0400 |
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| @@ -0,0 +1,91 @@ +#!/usr/bin/env Rscript + +args = commandArgs(TRUE) +countDataPath = args[1] +statsDataPath = args[2] +logFC = args[3] +logCPM = args[4] +pValue = args[5] +fdr = args[6] + +clusterRow = args[7] +clusterCol = args[8] +hclustMethod = args[9] + +mgColumnNm = as.numeric(args[10]) +mgRowNm = as.numeric(args[11]) + +pdfWidth = as.numeric(args[12]) +pdfHeight = as.numeric(args[13]) + + +if(clusterRow == "Yes"){ + clusterRow = TRUE +} else { + clusterRow = NA +} + +if(clusterCol == "Yes"){ + clusterCol = TRUE +} else { + clusterCol = NA +} + +require(preprocessCore) +require(gplots) + +#prepare counts data -------------------------------------------------------- +countData = read.table(countDataPath, comment = "", + sep = "\t") + +groups = sapply(as.character(countData[1, -1]), strsplit, ":") +groups = as.vector(t(countData[1, -1])) + +names = as.vector(t(countData[2, -1])) + +countData = countData[-c(1,2), ] +rownames(countData) = countData[, 1] +countData = countData[, -1] +colnames(countData) = names + +countData = countData[, order(groups, names)] + +# prepare stats data ------------------------------------------------------ + +statsData = read.table(statsDataPath, sep = "\t", + header = T) + +colnames(statsData)[-1] = sapply(colnames(statsData)[-1], function(x){ + unlist(strsplit(x, ".", fixed = T))[3] +}) + +wh = which(abs(statsData$logFC) >= logFC & statsData$logCPM >= logCPM & statsData$PValue <= pValue & statsData$FDR <= fdr) + +for(i in 1:ncol(countData)){ + countData[,i] = as.numeric(countData[,i]) +} + +countDataNorm = normalize.quantiles(as.matrix(countData), copy = T) +countDataNormLog = log(countDataNorm + 1, 2) + +colnames(countDataNormLog) = colnames(countData) +rownames(countDataNormLog) = rownames(countData) + +#svg("heatmap.svg", width = 3+length(names), height = 1/2*length(wh)) +pdf("heatmap.pdf", width = pdfWidth, height = pdfHeight) + +heatmap.2( + countDataNormLog[wh, ], + density.info=c("none"), + hclustfun = function(x) hclust(x, method = hclustMethod), + distfun = function(x) as.dist(1-cor(t(x))), + col = bluered(50), + scale = "row", + trace = "none", + Rowv = clusterRow, + Colv = clusterCol, + margins = c(mgColumnNm, mgRowNm) +) + +dev.off() + |
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| diff -r 000000000000 -r bd8fd161908b test-data/count.matrix --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count.matrix Wed Jul 12 14:29:51 2017 -0400 |
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| diff -r 000000000000 -r bd8fd161908b test-data/heatmap.pdf |
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| Binary file test-data/heatmap.pdf has changed |
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| diff -r 000000000000 -r bd8fd161908b test-data/stats.data --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/stats.data Wed Jul 12 14:29:51 2017 -0400 |
| b |
| b'@@ -0,0 +1,1680 @@\n+Feature\tgr2-gr1:logFC\tgr2-gr1:logCPM\tgr2-gr1:PValue\tgr2-gr1:FDR\n+Cj0001\t0.251163140624812\t7.450466899601\t0.000210979477327028\t0.000648781213245567\n+Cj0002\t0.530387367681972\t9.73328197799141\t3.92647017615346e-62\t1.43316161429601e-60\n+Cj0003\t-0.141096118617414\t10.1328696827574\t3.23730270556559e-07\t1.49736397868998e-06\n+Cj0004c\t0.546789320738327\t4.27438964069929\t0.0101429432128199\t0.0223216152515204\n+Cj0005c\t-0.0386100455851845\t6.41352518261495\t0.713021814662884\t0.801314341913642\n+Cj0006\t0.0572262525537494\t6.34479964715941\t0.583897736817362\t0.685569440640805\n+Cj0007\t-0.0798748935714388\t10.1859689943891\t0.00666385884081241\t0.0156265628403967\n+Cj0008\t-0.255567171662445\t9.51034236301575\t5.54315407636418e-14\t4.11812198859091e-13\n+Cj0009\t-0.484759400409196\t9.62822097543145\t9.67052427932554e-50\t2.61884036532058e-48\n+Cj0010c\t-0.378190664513606\t6.51239940649276\t5.36839159626876e-05\t0.000183155708236247\n+Cj0011c\t-0.0936887877353404\t9.76634066448534\t0.00440155038839324\t0.0106487076399312\n+Cj0012c\t-0.197456901899823\t12.949347565317\t3.16490585700577e-60\t1.08446468039034e-58\n+Cj0013\t-0.364006157463179\t7.97565692061486\t2.10110931097026e-10\t1.246559198982e-09\n+Cj0014c\t0.229302522931033\t7.89915141545952\t7.3889787523684e-05\t0.000247133373012481\n+Cj0015c\t-0.156583554909941\t8.4000051205571\t0.00125756904417107\t0.003422136831707\n+Cj0016\t0.127083234386439\t6.79211799297971\t0.143007733647566\t0.22208899226952\n+Cj0017c\t-0.18352203902824\t7.09385501458378\t0.0164829285531994\t0.0345072781057629\n+Cj0018c\t-0.978590636036807\t4.54920036252744\t4.20719576672574e-07\t1.92476340390532e-06\n+Cj0019c\t0.127578640965301\t8.85951692547961\t0.00209796126661611\t0.00539585506454568\n+Cj0020c\t0.591304518222515\t8.57021062747079\t5.91328316644171e-38\t1.18195267100662e-36\n+Cj0021c\t0.015453274262304\t7.04717719970582\t0.872325116787744\t0.922313520835405\n+Cj0022c\t-0.0610807618230194\t4.65022647688166\t0.755664352572265\t0.836913224253848\n+Cj0023\t-0.00155879292653441\t8.93505784928644\t0.977619840313746\t1\n+Cj0024\t-0.11073341579623\t9.28136807636078\t0.0026924493181347\t0.00677754483530458\n+Cj0025c\t-0.288377536563003\t5.0502940017973\t0.0750668237772794\t0.128740752933659\n+Cj0026c\t-0.486893832008047\t7.05351465527707\t3.74572338965654e-10\t2.20669107762573e-09\n+Cj0027\t0.0615279240104964\t10.1819388112351\t0.029781050546858\t0.0580747780118173\n+Cj0028\t-0.0454073637059376\t7.83399574924162\t0.514654351321527\t0.624804523404804\n+Cj0029\t-0.205750222309521\t6.51086679060757\t0.0445561029712139\t0.0819383317510056\n+Cj0030\t0.203806772126169\t6.16664584501197\t0.0580593877928865\t0.103155250903975\n+Cj0031\t-0.022546617798866\t7.40873794226012\t0.758862272204966\t0.839900959151047\n+Cj0033\t-0.258372446631317\t6.90334794900954\t0.00201223850231749\t0.0052138093293072\n+Cj0034c\t-0.384103076190169\t7.73087023750986\t1.48504736931912e-08\t7.74346128287829e-08\n+Cj0035c\t-0.286286710162699\t4.63935723534391\t0.156641404154039\t0.239527247335729\n+Cj0036\t-0.036715548339173\t8.12389305588524\t0.498866673463925\t0.612726514078954\n+Cj0037c\t0.120131023920956\t8.6839310127116\t0.00951372918057541\t0.0210732866677917\n+Cj0038c\t0.869835832472237\t4.93917190533352\t1.23975792218773e-06\t5.32366637174731e-06\n+Cj0039c\t-0.243295673978174\t9.57034537165025\t4.4783463764191e-13\t3.18607778220664e-12\n+Cj0040\t0.253822924348461\t7.91895715827187\t1.00139722177811e-05\t3.76983393579695e-05\n+Cj0041\t-0.325279908421266\t8.69890329220657\t9.2596052853717e-14\t6.73024990222471e-13\n+Cj0042\t0.0850199671165459\t8.17843963926571\t0.106812978809227\t0.173946645412893\n+Cj0043\t-0.201750388999392\t8.57314218916993\t1.16907543313394e-05\t4.36195033829308e-05\n+Cj0044c\t0.09412638483492\t8.63442847229589\t0.0364988448933533\t0.069480227410363\n+Cj0045c\t-0.0655832609551803\t7.54260707321925\t0.324224706788124\t0.437364144790227\n+Cj0053c\t-0.33483860585757\t7.58803703245217\t1.82073447037724e-07\t8.63563044000955e-07\n+Cj0054c\t0.164049771960829\t7.77475968350957\t0.0241552526527\t0.0483969799569014\n+Cj0055c\t0.551168041619309\t7.26004484056475\t3.83461866183206e-14\t2.88714113597132e-13\n+Cj0056c\t0.11529059'..b'\n+Cjp07\t-0.201393832690504\t6.01913520892501\t0.0774727844265827\t0.132057670103789\n+Cjp08\t-0.0610565292975918\t3.02119869200662\t0.911902320795614\t0.956329791765044\n+Cjp09\t0.0789492050345755\t6.02329713096144\t0.551039972472727\t0.65523804092189\n+Cjp10\t-0.204083169510766\t8.45854384462665\t1.76391328367489e-05\t6.39656674576703e-05\n+Cjp11\t0.349068919311388\t11.9923156784728\t2.44148200321706e-81\t1.24219644951559e-79\n+Cjp12\t-0.208848577045457\t4.51381269704339\t0.301685213879788\t0.412584514937022\n+Cjp13\t-0.322231225736962\t6.38128949105107\t0.00107780166219975\t0.00296174957583205\n+Cjp14\t0.104210823178076\t3.16479010904796\t0.830375874138309\t0.893718649152705\n+Cjp15\t-0.209766151010146\t7.01286048574317\t0.00789098456236578\t0.0179768834195552\n+Cjp16\t-0.527469323690171\t3.83336481231359\t0.0368575810313408\t0.0698463640537486\n+Cjp17\t0.197329320131585\t1.50182740629166\t0.831812631474571\t0.894118699261078\n+Cjp19\t-0.585630413256889\t4.17239585352498\t0.00761744618229388\t0.017568258434164\n+Cjp20\t-0.114614424829157\t3.99582222380107\t0.636456459735365\t0.733332848591807\n+Cjp21\t-0.0686823737490038\t5.19856866137998\t0.681991688267342\t0.772126800135447\n+Cjp22\t-0.226540237060962\t6.66243106472528\t0.0110000844678772\t0.0240337364745386\n+Cjp23\t-0.353025723104197\t2.42783006043204\t0.391607487160007\t0.504611643086455\n+Cjp24\t-0.0152743402303605\t2.74468336782184\t0.999999999999776\t1\n+Cjp25\t0.0848310092076146\t5.31944191023014\t0.588852855180689\t0.69042174849747\n+Cjp26\t-0.166761557958878\t6.58792537916917\t0.0731730109983744\t0.126137048733337\n+Cjp27\t-0.858268961181644\t2.29538700484784\t0.0724567718900572\t0.125030750260438\n+Cjp28\t-0.224851950084201\t5.01702220568239\t0.217001981820457\t0.31167350511253\n+Cjp29\t0.734109496851576\t3.66100088606691\t0.00704870545765388\t0.0164143917661593\n+Cjp30\t-0.122166326183728\t3.81411418090365\t0.674943147226437\t0.765983072710674\n+Cjp32\t-0.0874439451768363\t5.97433497049163\t0.45896096308337\t0.575500714725152\n+Cjp33\t-0.328588828011158\t4.32966509182498\t0.124211315818702\t0.197866033453132\n+Cjp34\t-0.380671920243272\t5.85944326037467\t0.00133854890531683\t0.00361903963289366\n+Cjp35\t-0.430399681435943\t3.73450743410787\t0.100374637588678\t0.164579117686904\n+Cjp36\t-0.201563169939485\t2.70346212180279\t0.608925025674964\t0.708513595362623\n+Cjr01\t-0.102775882095673\t13.5422910142694\t7.20756779798992e-10\t4.17293321821554e-09\n+Cjr02\t-0.00199342109653863\t16.21381505212\t0.870136632410869\t0.921562930750092\n+Cjr03\t0.0716348479862328\t9.30066612687491\t0.0445037148480824\t0.0819317294187833\n+Cjr04\t-0.10277590228244\t13.5422910142694\t7.11640659274934e-10\t4.13441061218898e-09\n+Cjr05\t-0.00201720063842253\t16.2138690187805\t0.868521430782704\t0.921562930750092\n+Cjr06\t0.166954322200703\t8.79992007728668\t7.93557714601454e-05\t0.000263838297587295\n+Cjr07\t-0.102775979976485\t13.5422910142694\t6.77618864736138e-10\t3.95042386768047e-09\n+Cjr08\t-0.00201719911428346\t16.2138690187805\t0.86854118978017\t0.921562930750092\n+Cjr09\t0.172836846375826\t8.7634083905036\t5.48033049240918e-05\t0.000186264674023381\n+Cjs01\t0.194800216436614\t12.2901088394379\t2.34683500730423e-23\t2.83477408436245e-22\n+Cjs02\t0.520621450537711\t3.13408724707507\t0.128402772795709\t0.203193454782277\n+Cjs03\t0.168063147710577\t10.1054046632285\t2.1180899514834e-09\t1.19338021091967e-08\n+Cjt01\t0.0995906789925662\t5.04200992251548\t0.588231919020598\t0.690175675776089\n+Cjt02\t-0.124166329208327\t4.7344995351148\t0.506444192273288\t0.618864482406733\n+Cjt03\t-0.583941660254936\t4.13412515205323\t0.0085236436529396\t0.0191582298437558\n+Cjt04\t0.0724165206745971\t3.90781846125343\t0.870782546926074\t0.921562930750092\n+Cjt05\t-0.212480888910792\t6.56077639094446\t0.0223001487916176\t0.045165198819211\n+Cjt06\t0.146126727543698\t3.92584585167676\t0.62778126057736\t0.72542652202986\n+Cjt1\t0.435399237792385\t4.58359947584301\t0.0212662026694545\t0.0432799445842596\n+Cjt2\t-0.119492910275624\t4.842875582846\t0.522681436188141\t0.63078490717773\n+Cjt3\t-0.469303073374358\t4.74978787712401\t0.00808820116400837\t0.0184012056292277\n+Cjt4\t-0.280180139875651\t4.87572672286493\t0.107580248404089\t0.1745190696333\n' |