| Previous changeset 1:bcc7a4c4cc29 (2018-12-20) Next changeset 3:a8bedebab467 (2019-02-06) |
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Commit message:
planemo upload commit bd6bc95760db6832c77d4d2872281772c31f9039 |
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modified:
quantp.r quantp.xml |
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added:
test-data/mouse_protein_log_data.txt test-data/mouse_transcript_log_data.txt |
| b |
| diff -r bcc7a4c4cc29 -r ed0bb50d7ffe quantp.r --- a/quantp.r Thu Dec 20 16:06:05 2018 -0500 +++ b/quantp.r Wed Jan 09 16:59:24 2019 -0500 |
| [ |
| b'@@ -60,9 +60,9 @@\n dev.off();\n \n suppressWarnings(g <- autoplot(regmodel, label = FALSE)[[1]] +\n- geom_point(aes(text=sprintf("Residual: %.2f<br>Fitted value: %.2f<br>Gene: %s", .fitted, .resid, PE_TE_data$PE_ID)),\n- shape = 1, size = .1, stroke = .2) +\n- theme_light())\n+ geom_point(aes(text=sprintf("Residual: %.2f<br>Fitted value: %.2f<br>Gene: %s", .fitted, .resid, PE_TE_data$PE_ID)),\n+ shape = 1, size = .1, stroke = .2) +\n+ theme_light())\n saveWidget(ggplotly(g, tooltip= c("text")), file.path(gsub("\\\\.png", "\\\\.html", outplot)))\n \n outplot = paste(outdir,"/PE_TE_lm_2.png",sep="",collapse="");\n@@ -74,9 +74,9 @@\n dev.off();\n \n suppressWarnings(g <- autoplot(regmodel, label = FALSE)[[2]] +\n- geom_point(aes(text=sprintf("Standarized residual: %.2f<br>Theoretical quantile: %.2f<br>Gene: %s", .qqx, .qqy, PE_TE_data$PE_ID)),\n- shape = 1, size = .1) +\n- theme_light())\n+ geom_point(aes(text=sprintf("Standarized residual: %.2f<br>Theoretical quantile: %.2f<br>Gene: %s", .qqx, .qqy, PE_TE_data$PE_ID)),\n+ shape = 1, size = .1) +\n+ theme_light())\n saveWidget(ggplotly(g, tooltip = "text"), file.path(gsub("\\\\.png", "\\\\.html", outplot)))\n \n \n@@ -91,9 +91,9 @@\n cd_cont_neg <- function(leverage, level, model) {-cd_cont_pos(leverage, level, model)}\n \n suppressWarnings(g <- autoplot(regmodel, label = FALSE)[[4]] +\n- aes(label = PE_TE_data$PE_ID) + \n- geom_point(aes(text=sprintf("Leverage: %.2f<br>Standardized residual: %.2f<br>Gene: %s", .hat, .stdresid, PE_TE_data$PE_ID))) +\n- theme_light())\n+ aes(label = PE_TE_data$PE_ID) + \n+ geom_point(aes(text=sprintf("Leverage: %.2f<br>Standardized residual: %.2f<br>Gene: %s", .hat, .stdresid, PE_TE_data$PE_ID))) +\n+ theme_light())\n saveWidget(ggplotly(g, tooltip = "text"), file.path(gsub("\\\\.png", "\\\\.html", outplot)))\n \n cat(\'<table border=1 cellspacing=0 cellpadding=5 style="table-layout:auto; ">\', file = htmloutfile, append = TRUE);\n@@ -215,7 +215,7 @@\n cooksd_df[cooksd_df$cooksd > cutoff,]$colors <- "red"\n \n g <- ggplot(cooksd_df, aes(x = index, y = cooksd, label = row.names(cooksd_df), color=as.factor(colors), \n- text=sprintf("Gene: %s<br>Cook\'s Distance: %.3f", row.names(cooksd_df), cooksd))) +\n+ text=sprintf("Gene: %s<br>Cook\'s Distance: %.3f", row.names(cooksd_df), cooksd))) +\n ggtitle("Influential Obs. by Cook\'s distance") + xlab("Observations") + ylab("Cook\'s Distance") + \n #xlim(0, 3000) + ylim(0, .15) + \n scale_shape_discrete(solid=F) +\n@@ -275,10 +275,10 @@\n png(outplot, width = 10, height = 10, units = \'in\', res=300);\n # bitmap(outplot,"png16m");\n suppressWarnings(g <- ggplot(PE_TE_data_no_outlier, aes(x=TE_abundance, y=PE_abundance, label=PE_ID)) + geom_smooth() + \n- xlab("Transcript abundance log fold-change") + ylab("Protein abundance log fold-change") + \n- xlim(min_lim,max_lim) + ylim(min_lim,max_lim) +\n- geom_point(aes(text=sprintf("Gene: %s<br>Transcript Abundance (log fold-change): %.3f<br>Protein Abundance (log fold-change): %.3f",\n- PE_ID, TE_abundance, PE_abundance))))\n+ xlab("Transcript abundance log fold-change") + ylab("Protein abundance log fold-change") + \n+ xlim(min_lim,max_lim) + ylim(min_lim,max_lim) +\n+ geom_point(aes(text=sprintf("Gene: %s<br>Transcript Abundance (log fold-change): %.3f<br>Protein Abundance (log fold-change): %.3f",\n+ PE_ID, TE_abundance, PE_abundance))))\n suppressMessages(plot(g))\n suppressMessages(saveWidget(ggplotly(g, tooltip="text"), file.path(gsub("\\\\.png", "\\\\.html", outplot))))\n dev.off();\n@@ -440,9 +440,9 @@\n \n # Interactive plot for k-means clust'..b'enes, LogFold, -log10(TE_pval), TE_pval))) +\n xlab("log2 fold change") + ylab("-log10 p-value") + \n geom_point(shape=1, size = 1.5, stroke = .2) +\n@@ -974,28 +974,33 @@\n \n # TE Boxplot\n outplot = paste(outdir,"/Box_TE.png",sep="",collape="");\n+ multisample_boxplot(TE_df, sampleinfo_df, outplot, "Yes", "Samples", "Transcript Abundance data");\n+ lines <- extractWidgetCode(outplot)\n+ prescripts <- c(prescripts, lines$prescripts)\n+ postscripts <- c(postscripts, lines$postscripts)\n cat(\'<table border=1 cellspacing=0 cellpadding=5 style="table-layout:auto; ">\\n\',\n \'<tr bgcolor="#7a0019"><th><font color=#ffcc33>Boxplot: Transcriptome data</font></th><th><font color=#ffcc33>Boxplot: Proteome data</font></th></tr>\\n\',\n- "<tr><td align=center>", \'<img src="Box_TE.png" width=500 height=500></td>\\n\', file = htmloutfile, append = TRUE);\n- multisample_boxplot(TE_df, sampleinfo_df, outplot, "Yes", "Samples", "Transcript Abundance data");\n+ "<tr><td align=center>", \'<img src="Box_TE.png" width=500 height=500>\', lines$widget_div, \'</td>\\n\', file = htmloutfile, append = TRUE);\n \n # PE Boxplot\n outplot = paste(outdir,"/Box_PE.png",sep="",collape="");\n- cat("<td align=center>", \'<img src="Box_PE.png" width=500 height=500></td></tr></table>\\n\', file = htmloutfile, append = TRUE);\n multisample_boxplot(PE_df, sampleinfo_df, outplot, "Yes", "Samples", "Protein Abundance data");\n- \n+ lines <- extractWidgetCode(outplot)\n+ postscripts <- c(postscripts, lines$postscripts)\n+ cat("<td align=center>", \'<img src="Box_PE.png" width=500 height=500>\', lines$widget_div, \n+ \'</td></tr></table>\\n\', file = htmloutfile, append = TRUE);\n cat(\'<hr/><h2 id="corr_data"><font color=#ff0000>CORRELATION</font></h2>\\n\',\n file = htmloutfile, append = TRUE);\n \n # TE PE scatter\n+ PE_TE_data = data.frame(PE_df, TE_df);\n+ colnames(PE_TE_data) = c("PE_ID","PE_abundance","TE_ID","TE_abundance");\n outplot = paste(outdir,"/TE_PE_scatter.png",sep="",collape="");\n cat(\'<table border=1 cellspacing=0 cellpadding=5 style="table-layout:auto; "> <tr bgcolor="#7a0019"><th><font color=#ffcc33>Scatter plot between Proteome and Transcriptome Abundance</font></th></tr>\\n\', file = htmloutfile, append = TRUE);\n singlesample_scatter(PE_TE_data, outplot); \n lines <- extractWidgetCode(outplot);\n postscripts <- c(postscripts, lines$postscripts);\n- cat("<tr><td align=center>", \'<img src="TE_PE_scatter.png" width=800 height=800>\', lines$widget_div, \'</td></tr>\\n\', file = htmloutfile, append = TRUE);\n- PE_TE_data = data.frame(PE_df, TE_df);\n- colnames(PE_TE_data) = c("PE_ID","PE_abundance","TE_ID","TE_abundance");\n+ cat("<tr><td align=center>", \'<img src="TE_PE_scatter.png" width=800 height=800>\', gsub(\'width:500px;height:500px\', \'width:800px;height:800px\' , lines$widget_div), \'</td></tr>\\n\', file = htmloutfile, append = TRUE);\n \n # TE PE Cor\n cat("<tr><td align=center>", file = htmloutfile, append = TRUE);\n@@ -1014,7 +1019,9 @@\n extractWidgetCode(paste(outdir,"/PE_TE_lm_2.png",sep="",collapse=""))$postscripts,\n extractWidgetCode(paste(outdir,"/PE_TE_lm_5.png",sep="",collapse=""))$postscripts,\n extractWidgetCode(paste(outdir,"/PE_TE_lm_cooksd.png",sep="",collapse=""))$postscripts,\n- extractWidgetCode(paste(outdir,"/AbundancePlot_scatter_without_outliers.png",sep="",collapse=""))$postscripts));\n+ extractWidgetCode(paste(outdir,"/AbundancePlot_scatter_without_outliers.png",sep="",collapse=""))$postscripts,\n+ gsub(\'data-for="html\', \'data-for="secondhtml"\', \n+ extractWidgetCode(paste(outdir,"/TE_PE_scatter.png",sep="",collapse=""))$postscripts)))\n \n cat(\'<hr/><h2 id="cluster_data"><font color=#ff0000>CLUSTER ANALYSIS</font></h2>\\n\',\n file = htmloutfile, append = TRUE);\n' |
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| diff -r bcc7a4c4cc29 -r ed0bb50d7ffe quantp.xml --- a/quantp.xml Thu Dec 20 16:06:05 2018 -0500 +++ b/quantp.xml Wed Jan 09 16:59:24 2019 -0500 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="quantp" name="QuanTP" version="1.1.0"> +<tool id="quantp" name="QuanTP" version="1.1.1"> <description>Correlation between protein and transcript abundances</description> <requirements> <requirement type="package" version="1.10.4">r-data.table</requirement> @@ -7,7 +7,7 @@ <requirement type="package" version="3.0.0">r-ggplot2</requirement> <requirement type="package" version="0.4.5">r-ggfortify</requirement> <requirement type="package" version="4.8.0">r-plotly</requirement> - <requirement type="package" version="0.6.1.2">r-d3heatmap</requirement> + <requirement type="package" version="0.6.1.1">r-d3heatmap</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ Rscript '$__tool_directory__/quantp.r' @@ -114,6 +114,24 @@ </assert_contents> </output> </test> + <test> + <conditional name="experiment_design_option"> + <param name="sample_type" value="logfold"/> + <param name="correction_method" value="BH"/> + <param name="volcano_with" value="pval"/> + </conditional> + <param name="pe_exp" value="mouse_protein_log_data.txt" ftype="tabular" /> + <param name="te_exp" value="mouse_transcript_log_data.txt" ftype="tabular" /> + <param name="cooksd_upper" value="4"/> + <param name="nclust" value="4"/> + <param name="hm_nclust" value="5"/> + <output name="html_file"> + <assert_contents> + <has_text text="SAMPLE DISTRIBUTION" /> + <has_text text="plotly" /> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[ |
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| diff -r bcc7a4c4cc29 -r ed0bb50d7ffe test-data/mouse_protein_log_data.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mouse_protein_log_data.txt Wed Jan 09 16:59:24 2019 -0500 |
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| b'@@ -0,0 +1,3554 @@\n+Gene\tlogFold_proB_preproB\n+Pcx\t-0.215265223\n+Cers2\t0.06298783\n+Nsa2\t0.10744011\n+Tom1\t-0.144979097\n+Pmvk\t0.257954334\n+Nampt\t0.258178827\n+Ube2d3\t0.028890123\n+Tspan3\t-0.513643194\n+Nmt1\t-0.000295754\n+Pde12\t-0.163894925\n+Ranbp10\t-0.104972012\n+Eri1\t0.41176789\n+Cul4a\t0.118386345\n+Sde2\t-0.279915784\n+Crtc2\t0.318750624\n+Gpx1\t-0.688658971\n+Atp13a1\t-0.109330393\n+B2m\t0.737042021\n+Gpx4\t0.115972019\n+Cacybp\t-0.018669293\n+Sh3gl1\t-0.076607495\n+Bcl2\t-0.598897838\n+Syf2\t0.158267287\n+Spg7\t0.520539914\n+Cirbp\t-0.370333441\n+Ccdc114\t0.667889424\n+Ccdc115\t-0.12539521\n+Cstf1\t0.02477631\n+Rabif\t-0.184199945\n+Cstf3\t0.150892312\n+Cstf2\t-0.07130932\n+Hspd1\t0.109325823\n+Akt2\t0.263571665\n+Lamc1\t-0.054221843\n+Wdr82\t0.039155178\n+Rnf126\t-0.049235527\n+Uqcrb\t0.277656319\n+Wdr89\t0.309720999\n+Top3b\t-0.311153494\n+Exosc10\t0.075792817\n+Cebpb\t0.279918139\n+Naa15\t-0.044017153\n+Naa10\t0.019126795\n+Vps18\t-0.681137551\n+Fubp3\t-0.671449149\n+Fubp1\t0.101441633\n+Slu7\t0.045571542\n+Ezr\t-0.181424454\n+Slc25a12\t0.795986319\n+Sf3a1\t-0.195715138\n+Sap18\t-0.082584304\n+Sf3a3\t-0.052605802\n+Ccar1\t-0.115152501\n+Ccar2\t-0.171779144\n+Pitpna\t-0.559275401\n+Pitpnb\t-0.259196255\n+Ubp1\t-0.488899947\n+Rab27a\t-0.624541042\n+Cog8\t0.552417456\n+Aven\t-0.120449936\n+Rbm8a\t0.1391538\n+Ptrhd1\t-0.068203232\n+Cog3\t0.090436167\n+Cog2\t-0.392656478\n+Cog1\t0.231627847\n+Szrd1\t0.244030886\n+Cog7\t0.251115552\n+Tmed5\t-0.077922423\n+Cog5\t0.073079836\n+Max\t0.235418273\n+Rtf1\t-0.082298321\n+Rtf2\t-0.180401499\n+9130011E15Rik\t-0.338998954\n+Serpinh1\t0.617452668\n+Gm11273\t-0.049912797\n+Fto\t-0.330907224\n+Tmed2\t-0.337346617\n+Crtc1\t0.218809607\n+Nosip\t0.291867522\n+Mad2l1\t0.00140304\n+Snrpd3\t0.215724501\n+Snrpd2\t0.08489563\n+Snrpd1\t0.450069466\n+Tab1\t-0.023643291\n+Letm1\t-0.137322352\n+Scpep1\t0.526122971\n+Cyba\t-0.068303757\n+Ifi47\t0.898775642\n+Ndrg1\t-0.188344851\n+Mak16\t0.089999801\n+Tap1\t0.290951564\n+Ubap2\t0.063159206\n+Ppp1r7\t0.055401106\n+Tap2\t0.181550384\n+H13\t-0.45346534\n+Rpap3\t-0.030575446\n+Gga3\t0.061736059\n+Gga2\t-0.066192753\n+Flii\t-0.220704152\n+Lsm6\t0.198169684\n+Ptpn2\t-0.067657001\n+Kyat3\t0.477597585\n+Zfp622\t-0.033937136\n+Mrps2\t-0.17242683\n+Lama3\t0.0\n+Skiv2l2\t0.018798014\n+Slc7a5\t0.312561851\n+Plcl2\t0.671671065\n+Gng12\t-0.424253152\n+Sash3\t-1.39463533\n+Stx12\t-0.157527171\n+Arhgap11a\t0.112447939\n+Stx17\t0.208628356\n+Znhit3\t0.436770625\n+Stub1\t0.119773081\n+Tyms\t0.838896139\n+Fam104a\t0.195500022\n+AI314180\t0.247780507\n+Trnt1\t0.171968999\n+Rap2b\t-0.168032156\n+Mrpl11\t-0.041269681\n+Mrpl12\t0.11432299\n+Pdxk\t-0.611187809\n+Psmd9\t-0.210160134\n+Klf16\t0.079320057\n+Mrpl16\t0.19234941\n+Mrpl17\t0.0\n+Psmd5\t-0.313032343\n+Psmd4\t-0.021890955\n+Psmd7\t0.050047408\n+Psmd6\t0.392043666\n+Psmd1\t0.033601285\n+Psmd3\t0.159317808\n+Psmd2\t0.139191749\n+Agpat5\t-0.294616508\n+Ncl\t0.005410049\n+Ifrd1\t0.269977437\n+Lta4h\t-0.316019044\n+Lmna\t-0.198911761\n+Stam\t0.137150634\n+Phb2\t0.151722511\n+Prpf18\t0.094885988\n+Supt16\t0.048007355\n+Ermp1\t0.174998197\n+Cmas\t-0.599717795\n+Ubfd1\t-0.639834616\n+Gstp1\t0.441120135\n+Wdfy4\t0.669308971\n+Hba-a1\t1.208424301\n+Wdfy1\t0.059915922\n+Cox6b1\t-0.096497356\n+Pttg1\t0.335605569\n+Atp5f1\t0.125402434\n+Fam133b\t-0.450716258\n+Mras\t-1.356031874\n+Cbl\t-0.214277555\n+Commd2\t-0.188134397\n+Htatsf1\t-0.110332747\n+Snf8\t0.162427903\n+Imp3\t-0.129109962\n+H3f3b\t0.19155507\n+Clec12a\t-0.967010282\n+Larp4b\t-0.186649561\n+Rfc5\t0.151931495\n+Rfc4\t0.129912002\n+Uck2\t-0.292134219\n+Rfc1\t0.116536401\n+Rfc3\t0.214569923\n+Rfc2\t0.103829326\n+Apex1\t0.154397855\n+Acat1\t0.073411678\n+Acat3\t-0.538205588\n+Aldh1b1\t-0.110917575\n+Sars\t0.293718883\n+Usp25\t0.170018557\n+Asah1\t-0.407403016\n+Tcof1\t-0.14974705\n+Arl8b\t-0.307375134\n+Trim33\t-0.114277936\n+Ahnak\t0.069691172\n+Amdhd2\t-0.113235447\n+Efl1\t0.022742846\n+Ldlr\t-0.36033416\n+Dlat\t0.01757712\n+Smap1\t0.174311756\n+Ube3a\t-0.175096307\n+Dbnl\t0.139783806\n+Fam91a1\t-0.616247198\n+Zmynd8\t-0.449147435\n+Tigar\t0.472461791\n+Paf1\t-0.017087958\n+Gmnn\t0.140101904\n+Fam114a2\t-0.112215551\n+Slc7a6os\t0.090380599\n+Tpr\t-0.064049863\n+Aldoa\t0.318464889\n+Cmtr1\t0.294191907\n+Uqcrq\t0.332392823\n+Rlim\t-0.350160122\n+Cox6c\t-0.102884091\n+Gpsm1\t0.152517109\n+Kdm1a\t-0.627787864\n+Vav1\t-0.480185129\n+Kbtbd4\t0.138839398\n+Cd'..b'235166058\n+Pigs\t-0.255226612\n+Pdcl\t0.112293139\n+Caprin1\t0.00345975\n+Ndufs4\t0.027901441\n+Exosc5\t-0.041554636\n+Wapl\t0.05162683\n+Ogdh\t-0.041181196\n+Gsto1\t-1.330179383\n+Trmt10c\t-0.082422958\n+Fam98b\t0.11961115\n+Ndufs7\t-0.146245097\n+Acaa1a\t-0.180908987\n+Tmx1\t-0.094293314\n+Tmx3\t-0.269127943\n+Tmx2\t0.352320163\n+Aars2\t-0.128833505\n+Pbk\t0.088263694\n+Rad23b\t-0.280196971\n+Btf3\t-0.140693568\n+Ppp2ca\t-0.098291296\n+Scarb2\t-0.409639786\n+Ppp2cb\t-0.230312755\n+Fli1\t0.100092194\n+G3bp1\t-0.096922824\n+G3bp2\t-0.030939474\n+Mzb1\t1.559917574\n+Twnk\t0.0\n+Tor1aip1\t0.205023288\n+Sap130\t0.24979241\n+Tbce\t0.359427862\n+Tbcd\t0.002462066\n+Noc3l\t-0.036676488\n+Tbcb\t0.0797665\n+Tbca\t0.051903754\n+Runx3\t-1.273516763\n+Runx1\t0.169464474\n+Xpot\t0.173906442\n+Cdc123\t0.032436582\n+Gpkow\t-0.054388547\n+Txndc5\t-0.022810493\n+Bcl10\t0.084589449\n+Tmem43\t-0.420831979\n+Foxp1\t-0.550297683\n+Rbm27\t-0.1182722825\n+Was\t-0.150828396\n+Ptar1\t0.024848664\n+Anxa2\t0.334221583\n+Mcat\t-0.026379788\n+Faf1\t0.172335177\n+Golgb1\t-0.242358615\n+Gbf1\t0.145374796\n+Rreb1\t0.112102201\n+Idh3a\t0.080492589\n+Ddx42\t-0.143180319\n+Idh3b\t0.251247626\n+Idh3g\t0.211273857\n+Cd84\t0.939336459\n+Ccs\t-0.371100293\n+Rnf220\t-0.100077883\n+Rprd1b\t-0.01016239\n+Sipa1\t-0.036676223\n+Ssbp3\t-1.365947309\n+Dnajc1\t0.0\n+Pfdn1\t0.315879254\n+Mrpl24\t-0.015984234\n+Pfdn2\t0.106675231\n+Pfdn5\t0.133321448\n+Pfdn4\t0.274728056\n+Mrpl23\t0.480841098\n+Pfdn6\t0.119544821\n+Cops4\t0.022133431\n+Mrpl28\t0.184928901\n+Fam96b\t0.053171209\n+Pih1d1\t-0.16104598\n+Eps15l1\t0.133855416\n+Ppp3ca\t0.517969081\n+Acyp1\t0.036428698\n+Pts\t-0.348487844\n+Sec31a\t-0.115212016\n+Rack1\t0.303661479\n+Gabpb2\t-0.059371231\n+Rab1b\t0.04509072\n+Hcfc1\t-0.122395702\n+Rwdd1\t0.109058271\n+Hmg20a\t0.225460031\n+Ercc4\t0.08219843\n+Tmsb4x\t0.278970747\n+Ncln\t-0.438770681\n+Echs1\t-0.120163171\n+Faf2\t0.134980553\n+Tmem214\t-0.10650191\n+Ptbp3\t-0.427242998\n+Bpnt1\t0.059698619\n+Ptbp1\t-0.07325484\n+Itpk1\t-1.49244874\n+Chchd3\t-0.121881153\n+P4hb\t-0.407880053\n+Chchd1\t0.19570156\n+Chchd4\t-0.094669281\n+Arid1b\t-0.417512044\n+Arid1a\t-0.327399098\n+Mtpap\t-0.011178384\n+Dnajb11\t-0.175805706\n+Snrnp27\t0.182288107\n+Ranbp9\t-0.167993703\n+Urod\t0.486218075\n+Atrx\t-0.298521564\n+Tagln2\t-0.106975717\n+Ranbp1\t-0.191016486\n+Ranbp3\t0.185087598\n+Ranbp2\t-0.053122631\n+Ppm1g\t-0.080878261\n+Ppm1f\t-0.87671356\n+Akirin2\t0.04134399\n+Gclm\t-0.163939625\n+Ppm1b\t0.0\n+Rpl8\t0.212172181\n+Rpl9\t0.076812173\n+Rpl6\t0.088841766\n+Rpl7\t0.10912652\n+Rpl4\t0.132617707\n+Rpl5\t0.072286867\n+Rpl3\t0.071224529\n+Aldh2\t-0.568314182\n+Fibp\t0.208628356\n+Sdc4\t1.371992612\n+Ppp6c\t0.23872077\n+Ikbkg\t0.105248983\n+Mecr\t0.367315161\n+Aifm1\t0.278075211\n+Arglu1\t0.006576738\n+Alpl\t1.654281142\n+Ivd\t-0.642268271\n+Clpx\t-0.271814574\n+Samhd1\t-0.995425471\n+Seh1l\t0.229029127\n+Trim25\t0.033105027\n+Txndc17\t0.050256536\n+Mcrip2\t0.089195709\n+Atp6v1e1\t-0.094055941\n+Hprt\t0.318416342\n+Txndc12\t0.069779168\n+Fhl3\t-0.047693318\n+Fabp5\t-1.114452192\n+Nbn\t0.018355052\n+Lsm14b\t-1.003252072\n+Sart3\t-0.052668946\n+Sart1\t-0.044946561\n+Tes\t-1.353111849\n+Cops5\t-0.057046987\n+Gstz1\t-0.046224144\n+Ttc4\t-0.051372815\n+Rpl26\t0.134753278\n+Ttc1\t0.139685615\n+Emd\t0.021638972\n+Tle3\t-0.540779654\n+Psmd14\t0.125561194\n+Psmd11\t0.000297156\n+Psmd10\t-0.024881579\n+Psmd13\t0.121748817\n+Psmd12\t0.047384891\n+Suclg2\t-0.413003576\n+Suclg1\t-0.354229002\n+Adgrg1\t-0.828327644\n+Gatad2b\t-0.144872324\n+Gatad2a\t-0.117612183\n+Irgq\t0.167436217\n+Nup50\t0.085885567\n+Nup54\t-0.024274457\n+Hist1h4j\t0.739118757\n+Gm49322\t0.316197826\n+Atl3\t0.035415636\n+Atl2\t0.415408204\n+Endog\t-0.289161413\n+Rsl1d1\t0.186840266\n+Noc2l\t0.058441179\n+Sit1\t1.491196814\n+Arfgap3\t-0.211047934\n+Carmil2\t-0.188329566\n+Nup133\t0.226932638\n+Gm45799\t-0.026592793\n+Dnmt1\t0.388766805\n+Hsd17b10\t-0.077187334\n+Ung\t0.216226313\n+Sssca1\t0.139051662\n+Rfx7\t0.024594904\n+Fbxo41\t-0.788091214\n+Decr1\t-0.778623962\n+Hnrnph2\t0.0\n+Rpl29\t-0.017441981\n+Rpl28\t0.096168708\n+Myo1g\t-0.249141033\n+Rpl24\t0.193895279\n+Myo1e\t-0.60205333\n+Ifi209\t1.270900249\n+Rpl21\t0.094885988\n+Rpl23\t0.293918942\n+Rpl22\t0.034736844\n+Arf3\t0.179534048\n+Kdm5c\t-0.011858914\n+Ikbkap\t-0.516001115\n+F5\t0.410633144\n+Setd3\t0.126193222\n+Setd2\t0.569075878\n+Mndal\t1.101614432\n+Setd7\t-0.554664805\n' |
| b |
| diff -r bcc7a4c4cc29 -r ed0bb50d7ffe test-data/mouse_transcript_log_data.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mouse_transcript_log_data.txt Wed Jan 09 16:59:24 2019 -0500 |
| b |
| b'@@ -0,0 +1,3554 @@\n+Gene\tlogFold_proB_preproB\n+Pcx\t-2.2784116666666665\n+Cers2\t0.09282949999999998\n+Nsa2\t-0.17680649999999998\n+Tom1\t0.18414\n+Pmvk\t2.1532463999999996\n+Nampt\t0.3927926455555556\n+Ube2d3\t-0.16606370454347824\n+Tspan3\t-0.69420025\n+Nmt1\t-0.014821\n+Pde12\t0.215689\n+Ranbp10\t-0.501248\n+Eri1\t0.3608491000000001\n+Cul4a\t-0.18855159999999999\n+Sde2\t0.235638\n+Crtc2\t6.8662\n+Gpx1\t0.15080571428571435\n+Atp13a1\t-0.087365\n+B2m\t0.713986\n+Gpx4\t0.4603633333333333\n+Cacybp\t0.16028733333333334\n+Sh3gl1\t-0.389139\n+Bcl2\t-2.7282166666666665\n+Syf2\t-0.319676\n+Spg7\t0.10850800000000001\n+Cirbp\t0.075714\n+Ccdc114\t-0.227306\n+Ccdc115\t-1.34077\n+Cstf1\t-0.6868052366666667\n+Rabif\t0.0776701\n+Cstf3\t-0.0391965\n+Cstf2\t0.5335165714285715\n+Hspd1\t-0.01369299\n+Akt2\t-0.06621696585365856\n+Lamc1\t-0.9829918\n+Wdr82\t-0.040959199999999994\n+Rnf126\t0.0\n+Uqcrb\t0.0879794\n+Wdr89\t-0.01642205\n+Top3b\t0.0\n+Exosc10\t1.738803257142857\n+Cebpb\t-0.315509\n+Naa15\t0.22511550000000002\n+Naa10\t0.8014816666666666\n+Vps18\t-1.090045\n+Fubp3\t-0.32228102770588235\n+Fubp1\t0.02952788679245281\n+Slu7\t-0.030109444444444404\n+Ezr\t-0.308674\n+Slc25a12\t-0.05101691666666668\n+Sf3a1\t-0.0819402\n+Sap18\t-0.731672\n+Sf3a3\t0.265453\n+Ccar1\t0.41853833333333335\n+Ccar2\t0.0490184\n+Pitpna\t-1.0278746666666665\n+Pitpnb\t-0.543194\n+Ubp1\t-0.5833896000000001\n+Rab27a\t-0.6370971428571428\n+Cog8\t-0.3876043333333334\n+Aven\t-0.4489133\n+Rbm8a\t-0.259955\n+Ptrhd1\t-0.748024\n+Cog3\t-0.06112493833333333\n+Cog2\t1.7925556333333335\n+Cog1\t0.11708143529411764\n+Szrd1\t2.564985\n+Cog7\t-0.391159\n+Tmed5\t-0.24154155555555554\n+Cog5\t0.035345666666666664\n+Max\t1.137442375\n+Rtf1\t0.624934\n+Rtf2\t0.0839082\n+9130011E15Rik\t-1.32442\n+Serpinh1\t0.08293143809523806\n+Gm11273\t0.981315\n+Fto\t-0.12509155555555557\n+Tmed2\t-0.126668372\n+Crtc1\t-1.38401\n+Nosip\t0.04453161538461538\n+Mad2l1\t0.9823266666666667\n+Snrpd3\t-0.23968733333333328\n+Snrpd2\t0.661067\n+Snrpd1\t0.711066\n+Tab1\t-0.349305\n+Letm1\t-0.284479225\n+Scpep1\t-0.719828\n+Cyba\t-0.63762925\n+Ifi47\t-0.3543913416666667\n+Ndrg1\t-0.1659092\n+Mak16\t-0.332942\n+Tap1\t-0.46124800000000005\n+Ubap2\t0.20747949999999996\n+Ppp1r7\t0.26429299999999994\n+Tap2\t-0.7624599999999999\n+H13\t-0.16424025000000003\n+Rpap3\t0.00286533\n+Gga3\t0.03140524999999999\n+Gga2\t0.570022\n+Flii\t-0.210913\n+Lsm6\t0.38651075\n+Ptpn2\t-0.20451449888888887\n+Kyat3\t-0.030416268750000003\n+Zfp622\t-1.005893\n+Mrps2\t0.131197\n+Lama3\t-4.683203333333334\n+Skiv2l2\t-0.065326\n+Slc7a5\t-0.0499792\n+Plcl2\t-1.01464\n+Gng12\t-0.07534800000000003\n+Sash3\t-0.501526\n+Stx12\t-0.0444315\n+Arhgap11a\t0.6150915\n+Stx17\t0.3478975\n+Znhit3\t0.0995209\n+Stub1\t0.272933\n+Tyms\t0.4673140625\n+Fam104a\t-0.0363341\n+AI314180\t-0.05112193333333332\n+Trnt1\t-1.4134316714285713\n+Rap2b\t0.190532\n+Mrpl11\t0.32184\n+Mrpl12\t0.309226\n+Pdxk\t-2.87512\n+Psmd9\t0.0542652\n+Klf16\t-1.08153\n+Mrpl16\t0.524322\n+Mrpl17\t0.7466367777777778\n+Psmd5\t-0.03279675000000001\n+Psmd4\t-0.03342002000000001\n+Psmd7\t0.157587\n+Psmd6\t0.01720499999999997\n+Psmd1\t0.23941880000000001\n+Psmd3\t0.282667\n+Psmd2\t0.116475\n+Agpat5\t0.0460638\n+Ncl\t0.85742725\n+Ifrd1\t0.0330824\n+Lta4h\t-0.844549\n+Lmna\t-1.7677285714285715\n+Stam\t-0.047267799999999985\n+Phb2\t0.03839014285714275\n+Prpf18\t0.037186111111111114\n+Supt16\t0.371462\n+Ermp1\t2.6873454999999997\n+Cmas\t-0.08525194736842105\n+Ubfd1\t-0.2090855\n+Gstp1\t0.185692\n+Wdfy4\t0.4673972\n+Hba-a1\t0.0\n+Wdfy1\t1.1630655666666667\n+Cox6b1\t0.2857805\n+Pttg1\t0.8354621428571428\n+Atp5f1\t0.4740409\n+Fam133b\t-0.060619875\n+Mras\t0.3881015\n+Cbl\t-0.22743511111111112\n+Commd2\t0.24368533333333334\n+Htatsf1\t0.37532645\n+Snf8\t-0.06154\n+Imp3\t-0.0562441\n+H3f3b\t0.8993865\n+Clec12a\t-2.46229\n+Larp4b\t-0.34195644444444445\n+Rfc5\t1.57677\n+Rfc4\t0.3890468\n+Uck2\t-0.006983473333333346\n+Rfc1\t0.1260752\n+Rfc3\t1.03759\n+Rfc2\t-0.993016\n+Apex1\t0.7195379\n+Acat1\t-0.269034\n+Acat3\t0.66413\n+Aldh1b1\t1.1996566666666666\n+Sars\t0.22619766666666663\n+Usp25\t-0.198769\n+Asah1\t-1.2023113333333333\n+Tcof1\t-0.17296447636363635\n+Arl8b\t-0.09267060000000002\n+Trim33\t-0.1586332\n+Ahnak\t-1.09784\n+Amdhd2\t-0.196168\n+Efl1\t-0.1499726666666667\n+Ldlr\t0.326661\n+Dlat\t-0.107374\n+Smap1\t0.086381\n+Ube3a\t-0.0380724\n+Dbnl\t-0.14851479775\n+Fam91a1\t-1.2429'..b'-0.1649166425\n+Sap130\t0.227239\n+Tbce\t-0.120875875\n+Tbcd\t-0.006468066666666667\n+Noc3l\t-0.349217\n+Tbcb\t-0.490396\n+Tbca\t-0.09660772\n+Runx3\t-1.0566833333333332\n+Runx1\t-0.2201825\n+Xpot\t-0.6363852222222223\n+Cdc123\t0.4558834\n+Gpkow\t-0.590967775\n+Txndc5\t0.022232166666666667\n+Bcl10\t-0.540479\n+Tmem43\t-0.847105\n+Foxp1\t-0.16954697619047618\n+Rbm27\t0.22650550000000003\n+Was\t-0.901303\n+Ptar1\t0.554401\n+Anxa2\t-0.24246637179166666\n+Mcat\t-0.327409\n+Faf1\t0.610258\n+Golgb1\t0.08011570000000001\n+Gbf1\t0.1480988700000001\n+Rreb1\t-0.45929768000000004\n+Idh3a\t0.7245006666666667\n+Ddx42\t-0.259852\n+Idh3b\t-0.4081466666666667\n+Idh3g\t-0.346251\n+Cd84\t0.9192465555555555\n+Ccs\t-0.119755\n+Rnf220\t-0.5660696000000001\n+Rprd1b\t0.00033231500000001634\n+Sipa1\t-2.2508462000000002\n+Ssbp3\t-0.11558600000000001\n+Dnajc1\t0.22497324285714287\n+Pfdn1\t0.737715\n+Mrpl24\t-0.023638249999999986\n+Pfdn2\t-0.14381400000000003\n+Pfdn5\t-0.09995884000000001\n+Pfdn4\t0.3039296470588235\n+Mrpl23\t-0.34447\n+Pfdn6\t-0.015830636363636384\n+Cops4\t0.4416469090909091\n+Mrpl28\t0.207771\n+Fam96b\t0.5499606666666667\n+Pih1d1\t0.10895171428571429\n+Eps15l1\t-0.25218719999999994\n+Ppp3ca\t-1.283955\n+Acyp1\t0.23605799999999996\n+Pts\t-0.595665\n+Sec31a\t0.29207325714285715\n+Rack1\t0.305403\n+Gabpb2\t0.8276734750000001\n+Rab1b\t-0.167101\n+Hcfc1\t0.16304281999999998\n+Rwdd1\t0.872186\n+Hmg20a\t-0.6006196666666667\n+Ercc4\t-0.28091715000000006\n+Tmsb4x\t-0.832525\n+Ncln\t-0.3086744444444445\n+Echs1\t-0.499489\n+Faf2\t0.05156223000000002\n+Tmem214\t0.17944400000000002\n+Ptbp3\t0.3288864034482758\n+Bpnt1\t-0.48766600000000004\n+Ptbp1\t0.11496755555555557\n+Itpk1\t-0.35648864166666666\n+Chchd3\t0.6020658333333333\n+P4hb\t-0.9323325\n+Chchd1\t0.26925411111111114\n+Chchd4\t-1.35307\n+Arid1b\t-0.009907333333333332\n+Arid1a\t-0.40936750000000005\n+Mtpap\t-0.297466\n+Dnajb11\t-0.3844245142857143\n+Snrnp27\t0.687906\n+Ranbp9\t-0.00542127199999999\n+Urod\t0.1191506\n+Atrx\t-5.2948749999995325e-05\n+Tagln2\t3.69068725\n+Ranbp1\t0.5566005\n+Ranbp3\t-0.0895816\n+Ranbp2\t0.0919968\n+Ppm1g\t0.09490190000000001\n+Ppm1f\t-1.03352\n+Akirin2\t0.0295709\n+Gclm\t0.2621809333333333\n+Ppm1b\t-0.49205299999999996\n+Rpl8\t-0.245761\n+Rpl9\t0.016753812499999996\n+Rpl6\t-0.18800399999999998\n+Rpl7\t0.0\n+Rpl4\t-0.214932\n+Rpl5\t1.6046878333333334\n+Rpl3\t0.053364\n+Aldh2\t-0.38793016666666663\n+Fibp\t-0.7028201999999999\n+Sdc4\t5.61229\n+Ppp6c\t0.16231459999999992\n+Ikbkg\t-0.8633122916666666\n+Mecr\t0.30696660000000003\n+Aifm1\t0.3861485\n+Arglu1\t-0.005857249999999994\n+Alpl\t1.1891394285714285\n+Ivd\t-0.824091\n+Clpx\t-0.42636225\n+Samhd1\t-0.70295375\n+Seh1l\t-0.10341\n+Trim25\t-0.5166798233333333\n+Txndc17\t0.0696596\n+Mcrip2\t-0.429605\n+Atp6v1e1\t-0.27154725\n+Hprt\t1.10007\n+Txndc12\t0.308909\n+Fhl3\t-2.0566066666666667\n+Fabp5\t-4.40314\n+Nbn\t0.22016100000000002\n+Lsm14b\t-0.6606429\n+Sart3\t-1.0654934999999999\n+Sart1\t-0.419921\n+Tes\t-8.771367499999998\n+Cops5\t0.38093057142857145\n+Gstz1\t-0.739611894736842\n+Ttc4\t-0.820256\n+Rpl26\t-0.14413985714285715\n+Ttc1\t0.2277003\n+Emd\t0.11678116666666666\n+Tle3\t-0.6690147096774194\n+Psmd14\t0.495752\n+Psmd11\t0.3857849574468085\n+Psmd10\t0.0822515\n+Psmd13\t0.1649473125\n+Psmd12\t0.7071472999999999\n+Suclg2\t-0.176226375\n+Suclg1\t-0.3905775\n+Adgrg1\t-0.3180009466666667\n+Gatad2b\t0.559004125\n+Gatad2a\t-0.18546084210526317\n+Irgq\t0.500504\n+Nup50\t0.419899\n+Nup54\t-0.3776533076923077\n+Hist1h4j\t-2.01294\n+Gm49322\t-0.24985433333333332\n+Atl3\t0.2770283333333334\n+Atl2\t0.47337625\n+Endog\t0.025535\n+Rsl1d1\t-0.805379\n+Noc2l\t-3.4973229999999997\n+Sit1\t25.1184\n+Arfgap3\t0.05845969999999999\n+Carmil2\t-0.12305200000000001\n+Nup133\t0.540657\n+Gm45799\t0.02158122727272728\n+Dnmt1\t-1.16960175\n+Hsd17b10\t0.0108171\n+Ung\t0.2955725\n+Sssca1\t0.4232541818181818\n+Rfx7\t0.4713244\n+Fbxo41\t-0.0611444\n+Decr1\t-1.07918\n+Hnrnph2\t0.5367791666666666\n+Rpl29\t-0.48384679999999997\n+Rpl28\t0.0\n+Myo1g\t0.18636943750000007\n+Rpl24\t1.56556\n+Myo1e\t-0.7930799428571429\n+Ifi209\t0.736210325\n+Rpl21\t-0.13954333333333344\n+Rpl23\t-0.04415122222222221\n+Rpl22\t-0.3697045\n+Arf3\t-0.08459299999999997\n+Kdm5c\t0.01032378000000005\n+Ikbkap\t-0.33916\n+F5\t1.05445\n+Setd3\t-0.18152902999999998\n+Setd2\t0.01872838571428572\n+Mndal\t1.21181\n+Setd7\t-0.791121\n' |