# HG changeset patch
# User iuc
# Date 1542879780 18000
# Node ID ff7cd3c7c1dfc2107a6e59083374dffac4989137
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
diff -r 000000000000 -r ff7cd3c7c1df macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Thu Nov 22 04:43:00 2018 -0500
@@ -0,0 +1,148 @@
+
+ &1 | head -1 | cut -d' ' -f 2 ]]>
+
+string2numericvector = function(string){
+ #' Converts a string to a valid vector
+ #'
+ #' e.g. "-1,2:5,2" evaluates to c(-1,2,3,4,5,2)
+ #'
+ #' @param add string2vector function to safe environment
+ #' @return vector of integers
+ terms = unlist(strsplit(string, split=","))
+ res = lapply(terms, function(x){
+ if (grepl(":",x)){
+ l_r = as.integer(c(unlist(strsplit(x,split=":"))))
+ return(seq(l_r[1],l_r[2]))
+ }
+ return(as.integer(x))
+ })
+ return(c(unlist(res)))
+}
+
+string2textvector = function(string){
+ #' Converts a string to a valid string vector
+ #'
+ #' e.g. "red,yellow,white" evaluates to c("red","yellow","white")
+ return(unlist(strsplit(string,",")))
+}
+
+ 3
+ 0.2
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+ r-raceid
+ bioconductor-scran
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+ 10.1038/nature14966
+ 10.1038/nmeth.4662
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diff -r 000000000000 -r ff7cd3c7c1df macros_cluster.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros_cluster.xml Thu Nov 22 04:43:00 2018 -0500
@@ -0,0 +1,403 @@
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diff -r 000000000000 -r ff7cd3c7c1df macros_inspectclusters.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros_inspectclusters.xml Thu Nov 22 04:43:00 2018 -0500
@@ -0,0 +1,326 @@
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diff -r 000000000000 -r ff7cd3c7c1df macros_inspecttrajectories.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros_inspecttrajectories.xml Thu Nov 22 04:43:00 2018 -0500
@@ -0,0 +1,243 @@
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diff -r 000000000000 -r ff7cd3c7c1df macros_trajectory.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros_trajectory.xml Thu Nov 22 04:43:00 2018 -0500
@@ -0,0 +1,156 @@
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diff -r 000000000000 -r ff7cd3c7c1df raceid_trajectory.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/raceid_trajectory.xml Thu Nov 22 04:43:00 2018 -0500
@@ -0,0 +1,53 @@
+
+ generates lineage from prior clustering
+
+ macros.xml
+ macros_trajectory.xml
+
+
+
+
+ &1 > '$outlog'
+ ]]>
+
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+ use_log
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diff -r 000000000000 -r ff7cd3c7c1df scripts/cluster.R
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/cluster.R Thu Nov 22 04:43:00 2018 -0500
@@ -0,0 +1,156 @@
+#!/usr/bin/env R
+VERSION = "0.2"
+
+args = commandArgs(trailingOnly = T)
+
+if (length(args) != 1){
+ message(paste("VERSION:", VERSION))
+ stop("Please provide the config file")
+}
+
+suppressWarnings(suppressPackageStartupMessages(require(RaceID)))
+suppressWarnings(suppressPackageStartupMessages(require(scran)))
+source(args[1])
+
+
+do.filter <- function(sc){
+ if (!is.null(filt.lbatch.regexes)){
+ lar <- filt.lbatch.regexes
+ nn <- colnames(sc@expdata)
+ filt$LBatch <- lapply(1:length(lar), function(m){ return( nn[grep(lar[[m]], nn)] ) })
+ }
+
+ sc <- do.call(filterdata, c(sc, filt))
+
+ ## Get histogram metrics for library size and number of features
+ raw.lib <- log(colSums(as.matrix(sc@expdata)))
+ raw.feat <- log(rowSums(as.matrix(sc@expdata)))
+ filt.lib <- log(colSums(getfdata(sc)))
+ filt.feat <- log(rowSums(getfdata(sc)))
+
+ br <- 50
+ ## Determine limits on plots based on the unfiltered data
+ ## (doesn't work, R rejects limits and norm data is too different to compare to exp data
+ ## so let them keep their own ranges)
+
+ ## betterrange <- function(floatval){
+ ## return(10 * (floor(floatval / 10) + 1))
+ ## }
+
+ ## tmp.lib <- hist(raw.lib, breaks=br, plot=F)
+ ## tmp.feat <- hist(raw.feat, breaks=br, plot=F)
+
+ ## lib.y_lim <- c(0,betterrange(max(tmp.lib$counts)))
+ ## lib.x_lim <- c(0,betterrange(max(tmp.lib$breaks)))
+
+ ## feat.y_lim <- c(0,betterrange(max(tmp.feat$counts)))
+ ## feat.x_lim <- c(0,betterrange(max(tmp.feat$breaks)))
+
+ par(mfrow=c(2,2))
+ print(hist(raw.lib, breaks=br, main="ExpData Log(LibSize)")) # , xlim=lib.x_lim, ylim=lib.y_lim)
+ print(hist(raw.feat, breaks=br, main="ExpData Log(NumFeat)")) #, xlim=feat.x_lim, ylim=feat.y_lim)
+ print(hist(filt.lib, breaks=br, main="FiltData Log(LibSize)")) # , xlim=lib.x_lim, ylim=lib.y_lim)
+ print(hist(filt.feat, breaks=br, main="FiltData Log(NumFeat)")) # , xlim=feat.x_lim, ylim=feat.y_lim)
+
+ if (filt.use.ccorrect){
+ par(mfrow=c(2,2))
+ sc <- do.call(CCcorrect, c(sc, filt.ccc))
+ print(plotdimsat(sc, change=T))
+ print(plotdimsat(sc, change=F))
+ }
+ return(sc)
+}
+
+do.cluster <- function(sc){
+ sc <- do.call(compdist, c(sc, clust.compdist))
+ sc <- do.call(clustexp, c(sc, clust.clustexp))
+ if (clust.clustexp$sat){
+ print(plotsaturation(sc, disp=F))
+ print(plotsaturation(sc, disp=T))
+ }
+ print(plotjaccard(sc))
+ return(sc)
+}
+
+do.outlier <- function(sc){
+ sc <- do.call(findoutliers, c(sc, outlier.findoutliers))
+ if (outlier.use.randomforest){
+ sc <- do.call(rfcorrect, c(sc, outlier.rfcorrect))
+ }
+ print(plotbackground(sc))
+ print(plotsensitivity(sc))
+ print(plotoutlierprobs(sc))
+ ## Heatmaps
+ test1 <- list()
+ test1$side = 3
+ test1$line = 0 #1 #3
+
+ x <- clustheatmap(sc, final=FALSE)
+ print(do.call(mtext, c(paste("(Initial)"), test1))) ## spacing is a hack
+ x <- clustheatmap(sc, final=TRUE)
+ print(do.call(mtext, c(paste("(Final)"), test1))) ## spacing is a hack
+ return(sc)
+}
+
+do.clustmap <- function(sc){
+ sc <- do.call(comptsne, c(sc, cluster.comptsne))
+ sc <- do.call(compfr, c(sc, cluster.compfr))
+ return(sc)
+}
+
+
+mkgenelist <- function(sc){
+ ## Layout
+ test <- list()
+ test$side = 3
+ test$line = 0 #1 #3
+ test$cex = 0.8
+
+ df <- c()
+ options(cex = 1)
+ lapply(unique(sc@cpart), function(n){
+ dg <- clustdiffgenes(sc, cl=n, pvalue=genelist.pvalue)
+
+ dg.goi <- dg[dg$fc > genelist.foldchange,]
+ dg.goi.table <- head(dg.goi, genelist.tablelim)
+ df <<- rbind(df, cbind(n, dg.goi.table))
+
+ goi <- head(rownames(dg.goi.table), genelist.plotlim)
+ print(plotmarkergenes(sc, goi))
+ print(do.call(mtext, c(paste(" Cluster ",n), test))) ## spacing is a hack
+ test$line=-1
+ print(do.call(mtext, c(paste(" Sig. Genes"), test))) ## spacing is a hack
+ test$line=-2
+ print(do.call(mtext, c(paste(" (fc > ", genelist.foldchange,")"), test))) ## spacing is a hack
+
+ })
+ write.table(df, file=out.genelist, sep="\t", quote=F)
+}
+
+pdf(out.pdf)
+
+if (use.filtnormconf){
+ sc <- do.filter(sc)
+ message(paste(" - Source:: genes:",nrow(sc@expdata),", cells:",ncol(sc@expdata)))
+ message(paste(" - Filter:: genes:",nrow(sc@ndata),", cells:",ncol(sc@ndata)))
+ message(paste(" :: ",
+ sprintf("%.1f", 100 * nrow(sc@ndata)/nrow(sc@expdata)), "% of genes remain,",
+ sprintf("%.1f", 100 * ncol(sc@ndata)/ncol(sc@expdata)), "% of cells remain"))
+}
+
+if (use.cluster){
+ par(mfrow=c(2,2))
+ sc <- do.cluster(sc)
+
+ par(mfrow=c(2,2))
+ sc <- do.outlier(sc)
+
+ par(mfrow=c(2,2), mar=c(1,1,6,1))
+ sc <- do.clustmap(sc)
+
+ mkgenelist(sc)
+}
+
+dev.off()
+
+saveRDS(sc, out.rdat)
diff -r 000000000000 -r ff7cd3c7c1df scripts/clusterinspect.R
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/clusterinspect.R Thu Nov 22 04:43:00 2018 -0500
@@ -0,0 +1,121 @@
+#!/usr/bin/env R
+VERSION = "0.2"
+
+args = commandArgs(trailingOnly = T)
+
+if (length(args) != 1){
+ message(paste("VERSION:", VERSION))
+ stop("Please provide the config file")
+}
+
+suppressWarnings(suppressPackageStartupMessages(require(RaceID)))
+source(args[1])
+
+## layout
+test <- list()
+test$side = 3
+test$line = 3
+
+do.plotting <- function(sc){
+ print(plotmap(sc, final = FALSE, fr = FALSE))
+ print(do.call(mtext, c("Initial Clustering tSNE", test)))
+ print(plotmap(sc, final = TRUE, fr = FALSE))
+ print(do.call(mtext, c("Final Clustering tSNE", test)))
+ print(plotmap(sc, final = FALSE, fr = TRUE))
+ print(do.call(mtext, c("Initial Clustering Fruchterman-Reingold", test)))
+ print(plotmap(sc, final = TRUE, fr = TRUE))
+ print(do.call(mtext, c("Final Clustering Fruchterman-Reingold", test)))
+}
+
+
+do.inspect.symbolmap <- function(sc){
+ if (!is.null(plotsym.use.typeremoveregex)){
+ plotsym$types = sub(plotsym.use.typeremoveregex, "", colnames(sc@ndata))
+
+ if (!is.null(plotsym.use.typeremoveregex.subselect)){
+ plotsym$subset = plotsym$types[grep(plotsym.use.typeremoveregex.subselect, plotsym$types)]
+ }
+ }
+ plotsym$fr = FALSE
+ print(do.call(plotsymbolsmap, c(sc, plotsym)))
+ print(do.call(mtext, c("Symbols tSNE", test)))
+ plotsym$fr = TRUE
+ print(do.call(plotsymbolsmap, c(sc, plotsym)))
+ print(do.call(mtext, c("Symbols FR", test)))
+}
+
+do.inspect.diffgene <- function(sc){
+
+ getSubNames <- function(lob, sc){
+ use.names <- NULL
+ if (!is.null(lob$manual)){
+ use.names <- lob$manual
+ }
+ else if (!is.null(lob$regex)){
+ nm <- colnames(sc@ndata)
+ use.names <- nm[grep(lob$regex, nm)]
+ }
+ else if (!is.null(lob$cln)){
+ use.names <- names(sc@cpart)[sc@cpart %in% lob$cln]
+ }
+ if (is.null(use.names)){
+ stop("A or B names not given!")
+ }
+ return(use.names)
+ }
+
+ A <- getSubNames(gfdat.A.use, sc)
+ B <- getSubNames(gfdat.B.use, sc)
+
+ fdat <- getfdata(sc, n=c(A,B))
+ dexp <- diffexpnb(fdat, A=A, B=B)
+ ## options for diffexpnb are mostly about DESeq, ignore
+ plotdiffg$x = dexp
+ print(do.call(plotdiffgenesnb, c(plotdiffg)))
+ print(do.call(mtext, c("Diff Genes", test)))
+}
+
+
+do.inspect.genesofinterest <- function(sc){
+ if (is.null(plotexp$n)){ ## No title, and one gene? Use gene name
+ if (length(plotexp$g) == 1){
+ plotexp$n <- plotexp$g
+ } else {
+ plotexp$n <- paste(plotexp$g, collapse=", ")
+ }
+ }
+
+ title <- paste(":", plotexp$n)
+ plotexp$n <- ""
+
+ plotexp$logsc=FALSE; plotexp$fr = FALSE
+ print(do.call(plotexpmap, c(sc, plotexp)))
+ print(do.call(mtext, c(paste("tSNE", title), test)))
+
+ plotexp$logsc=TRUE; plotexp$fr = FALSE
+ print(do.call(plotexpmap, c(sc, plotexp)))
+ print(do.call(mtext, c(paste("tSNE (Log)", title), test)))
+
+ plotexp$logsc=FALSE; plotexp$fr = TRUE
+ print(do.call(plotexpmap, c(sc, plotexp)))
+ print(do.call(mtext, c(paste("FR", title), test)))
+
+ plotexp$logsc=TRUE; plotexp$fr = TRUE
+ print(do.call(plotexpmap, c(sc, plotexp)))
+ print(do.call(mtext, c(paste("FR (Log)", title), test)))
+
+ if (!is.null(plotmarkg$samples)){
+ reg <- plotmarkg$samples
+ plotmarkg$samples <- sub("(\\_\\d+)$","", colnames(sc@ndata))
+ }
+ print(do.call(plotmarkergenes, c(sc, plotmarkg)))
+}
+
+sc <- in.rdat
+
+pdf(out.pdf)
+if (perform.plotting) do.plotting(sc)
+if (perform.symbolmap) do.inspect.symbolmap(sc)
+if (perform.genesofinterest) do.inspect.genesofinterest(sc)
+if (perform.diffgene) do.inspect.diffgene(sc)
+dev.off()
diff -r 000000000000 -r ff7cd3c7c1df scripts/pseudotemporal.R
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/pseudotemporal.R Thu Nov 22 04:43:00 2018 -0500
@@ -0,0 +1,58 @@
+#!/usr/bin/env R
+VERSION = "0.1"
+
+args = commandArgs(trailingOnly = T)
+
+if (length(args) != 1){
+ message(paste("VERSION:", VERSION))
+ stop("Please provide the config file")
+}
+
+suppressWarnings(suppressPackageStartupMessages(require(RaceID)))
+source(args[1])
+
+test <- list()
+test$side = 3
+test$line = 3
+second <- test
+second$cex = 0.5
+second$line = 2.5
+
+
+do.pseudotemp <- function(sc){
+ pdf(out.pdf)
+ ltr <- Ltree(sc)
+ ltr <- compentropy(ltr)
+ ltr <- do.call(projcells, c(ltr, pstc.projc))
+ ltr <- do.call(projback, c(ltr, pstc.projb))
+ ltr <- lineagegraph(ltr)
+ ltr <- do.call(comppvalue, c(ltr, pstc.comppval))
+ x <- do.call(compscore, c(ltr, pstc.compscore))
+ print(do.call(mtext, c("Compute Score", test)))
+ print(do.call(mtext, c("No. of inter-cluster links / Delta median entropy of each cluster / StemID2 score (combination of both)", second)))
+ plotdistanceratio(ltr)
+ print(do.call(mtext, c("Cell-to-Cell Distance Ratio", test)))
+ print(do.call(mtext, c("Original vs High-dimensional Embedded Space", second)))
+ do.call(plotgraph, c(ltr, pstc.plotgraph))
+ print(do.call(mtext, c("Lineage Trajectories ", test)))
+ print(do.call(mtext, c("Colour = Level of Significance, Width = Link Score ", second)))
+ plotspantree(ltr)
+ print(do.call(mtext, c("Minimum Spanning Tree", test)))
+ plotprojections(ltr)
+ print(do.call(mtext, c("Minimum Spanning Tree", test)))
+ print(do.call(mtext, c("Cells Projected onto Links", second)))
+ test$side = 4
+ test$line = 0
+ plotlinkscore(ltr)
+ print(do.call(mtext, c("Link Score", test)))
+ projenrichment(ltr)
+ print(do.call(mtext, c("Enrichment Ratios", test)))
+ dev.off()
+
+ return(ltr)
+}
+
+ltr <- do.pseudotemp(in.rdat)
+
+
+saveRDS(ltr, out.rdat)
diff -r 000000000000 -r ff7cd3c7c1df scripts/trajectoryinspect.R
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/trajectoryinspect.R Thu Nov 22 04:43:00 2018 -0500
@@ -0,0 +1,134 @@
+#!/usr/bin/env R
+VERSION = "0.2"
+
+args = commandArgs(trailingOnly = T)
+
+if (length(args) != 1){
+ message(paste("VERSION:", VERSION))
+ stop("Please provide the config file")
+}
+
+suppressWarnings(suppressPackageStartupMessages(require(RaceID)))
+suppressWarnings(suppressPackageStartupMessages(require(FateID)))
+source(args[1])
+
+test <- list()
+test$side = 3
+test$line = 2.5
+second <- test
+second$cex = 0.5
+second$line = 2.5
+
+do.trajectoryinspection.stemID <- function(ltr){
+ makeBranchLink <- function(i,j,k){
+ ingoing <- paste(sort(c(i,j)), collapse=".")
+ outgoing <- paste(sort(c(j,k)), collapse=".")
+ messed <- sort(c(ingoing,outgoing))
+ return(list(messed[[1]], messed[[2]]))
+ }
+
+ zzz <- do.call(getproj, c(ltr, trjsid.getproj))
+ bra <- branchcells(
+ ltr,
+ do.call("makeBranchLink", as.list(trjsid.branchcells.ijk))
+ )
+ write.table(
+ head(bra$diffgenes$z, trjsid.numdiffgenes),
+ file=out.diffgenes)
+
+ par(mfrow = c(2,2), cex=0.5)
+ print(do.call(plotmap, c(bra$scl, final=FALSE, fr=FALSE)))
+ print(do.call(mtext, c("Initial Clusters (tSNE)", test)))
+ print(do.call(plotmap, c(bra$scl, final=TRUE, fr=FALSE)))
+ print(do.call(mtext, c("Final Clusters (tSNE)", test)))
+ print(do.call(plotmap, c(bra$scl, final=FALSE, fr=TRUE)))
+ print(do.call(mtext, c("Initial Clusters (F-R)", test)))
+ print(do.call(plotmap, c(bra$scl, final=TRUE, fr=TRUE)))
+ print(do.call(mtext, c("Final Clusters (F-R)", test)))
+}
+
+do.trajectoryinspection.fateID <- function(ltr){
+ n <- do.call(cellsfromtree, c(ltr, trjfid.cellsfrom))
+ x <- getfdata(ltr@sc)
+
+ trjfid.filterset$x = x
+ trjfid.filterset$n = n$f
+ fs <- do.call(filterset, c(trjfid.filterset))
+ trjfid.getsom$x = fs
+ s1d <- do.call(getsom, c(trjfid.getsom))
+ trjfid.procsom$s1d = s1d
+ ps <- do.call(procsom, c(trjfid.procsom))
+
+ y <- ltr@sc@cpart[n$f]
+ fcol <- ltr@sc@fcol
+
+ trjfid.plotheat$xpart = y
+ trjfid.plotheat$xcol = fcol
+
+ ##Plot average z-score for all modules derived from the SOM:
+ trjfid.plotheat$x = ps$nodes.z
+ trjfid.plotheat$ypart = unique(ps$nodes)
+ print(do.call(plotheatmap, c(trjfid.plotheat)))
+ print(do.call(mtext, c("Average z-score for all modules derived from SOM", test)))
+ ##Plot z-score profile of each gene ordered by SOM modules:
+ trjfid.plotheat$x = ps$all.z
+ trjfid.plotheat$ypart = ps$nodes
+ print(do.call(plotheatmap, c(trjfid.plotheat)))
+ print(do.call(mtext, c("z-score profile of each gene ordered by SOM modules", test)))
+ ##Plot normalized expression profile of each gene ordered by SOM modules:
+ trjfid.plotheat$x = ps$all.e
+ trjfid.plotheat$ypart = ps$nodes
+ print(do.call(plotheatmap, c(trjfid.plotheat)))
+ print(do.call(mtext, c("Normalized expression profile of each gene ordered by SOM modules", test)))
+ ##Plot binarized expression profile of each gene (z-score < -1, -1 < z-score < 1, z-score > 1):
+ trjfid.plotheat$x = ps$all.b
+ trjfid.plotheat$ypart = ps$nodes
+ print(do.call(plotheatmap, c(trjfid.plotheat)))
+ print(do.call(mtext, c("Binarized expression profile of each gene", test)))
+ ## This should be written out, and passed back into the tool
+ ## to perform sominspect
+ return(list(fs=fs,ps=ps,y=y,fcol=fcol,nf=n$f))
+}
+
+do.trajectoryinspection.fateID.sominspect <- function(domo){
+ g <- trjfidsomi.use.genes
+ if (class(g) == "numeric"){
+ g <- names(ps$nodes)[ps$nodes %in% g]
+ }
+
+ typ = NULL
+ if (!is.null(trjfidsomi.use.types)){
+ typ = sub(trjfidsomi.use.types,"", domo$nf)
+ }
+
+ trjfidsomi$x = domo$fs
+ trjfidsomi$y = domo$y
+ trjfidsomi$g = g
+ trjfidsomi$n = domo$nf
+ trjfidsomi$col = domo$fcol
+ trjfidsomi$types = typ
+
+ ## The average pseudo-temporal expression profile of this group
+ ## can be plotted by the function plotexpression:
+ par(mfrow = c(1,1))
+ test$cex = 1
+ second$line = 1.5
+ if (trjfidsomi$name == "Title") trjfidsomi$name = ""
+ print(do.call(plotexpression, c(trjfidsomi)))
+ mess2 <- paste(c(trjfidsomi.use.genes), collapse=", ")
+ mess1 <- "Average pseudo-temporal expression profile"
+ print(do.call(mtext, c(mess1, test)))
+ print(do.call(mtext, c(mess2, second)))
+}
+
+ltr <- in.rdat
+
+pdf(out.pdf)
+if (perform.stemID) do.trajectoryinspection.stemID(ltr)
+if (perform.fateID) {
+ domo <- do.trajectoryinspection.fateID(ltr)
+ if (perform.fateID.sominspect) {
+ do.trajectoryinspection.fateID.sominspect(domo)
+ }
+}
+dev.off()
diff -r 000000000000 -r ff7cd3c7c1df test-data/intestinal.filter.pdf
Binary file test-data/intestinal.filter.pdf has changed
diff -r 000000000000 -r ff7cd3c7c1df test-data/intestinal.genelist
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/intestinal.genelist Thu Nov 22 04:43:00 2018 -0500
@@ -0,0 +1,201 @@
+n mean.ncl mean.cl fc pv padj
+ENSDARG00000108798 1 0.13225291542414 22.6067842060994 170.935998904815 5.63439752001819e-20 3.43529216795509e-16
+ENSDARG00000109030 1 0.186711263967539 34.6842724288799 185.764220603798 2.48233981248329e-19 7.56741291835532e-16
+ENSDARG00000108379 1 0.168199368419563 24.3874482842581 144.991319012715 4.11994031997326e-19 8.37309204362565e-16
+ENSDARG00000107599 1 0.194980763882093 20.9729826342942 107.564367975175 3.56470297051077e-18 5.43349850280104e-15
+ENSDARG00000107321 1 0.1 1.94683879586459 19.4683879586459 1.39905888784068e-09 1.70601240783292e-06
+ENSDARG00000105564 1 0.1 1.72137476189456 17.2137476189456 5.11677986670882e-09 5.19950114122061e-06
+ENSDARG00000090447 1 0.1 1.4302236712519 14.302236712519 3.51620742912878e-08 3.06261667077116e-05
+ENSDARG00000079591 1 0.11578454541401 1.47825950354764 12.767330028907 4.83701028926633e-08 3.6864064667071e-05
+ENSDARG00000107138 1 0.118643244515052 1.63372529702772 13.7700659123533 8.59237265783686e-08 5.36793599520202e-05
+ENSDARG00000041060 1 0.11578454541401 1.4382199783801 12.421519411226 8.84781911763433e-08 5.36793599520202e-05
+ENSDARG00000077004 1 0.1 1.29299827494356 12.9299827494356 1.0364347799037e-07 5.36793599520202e-05
+ENSDARG00000100003 1 0.1 1.29775216728225 12.9775216728225 1.05650700249999e-07 5.36793599520202e-05
+ENSDARG00000102310 1 0.129577145917004 1.72085266498654 13.2805260743185 1.20446928962954e-07 5.64896096836256e-05
+ENSDARG00000068650 1 0.115601615820105 1.27001296748153 10.9861177845289 2.26895176903151e-07 9.88128495413223e-05
+ENSDARG00000086678 1 0.128030253978187 1.35647794130946 10.5949796955067 3.16910756640577e-07 0.000122948041506908
+ENSDARG00000105857 1 0.105900327795989 1.37647789967886 12.9978625026598 3.22645344285801e-07 0.000122948041506908
+ENSDARG00000105159 1 0.1 1.16700756453584 11.6700756453584 3.44329675018825e-07 0.000123492825211163
+ENSDARG00000102997 1 0.125930886410326 1.40950930054417 11.1927211879659 3.75314178672153e-07 0.00012712725263134
+ENSDARG00000052615 1 0.109701288024116 1.2495211865536 11.3902143635625 4.65728278602572e-07 0.000149449753402099
+ENSDARG00000103046 1 0.111800655591977 1.27916812008568 11.441508221151 5.24275745356588e-07 0.000158237500570989
+ENSDARG00000105009 1 0.107892272707005 1.29390774186871 11.9925895470056 5.45020093815115e-07 0.000158237500570989
+ENSDARG00000069937 1 0.1 1.08683574177416 10.8683574177416 5.98190849813324e-07 0.000165780436877811
+ENSDARG00000034941 1 0.1 1.14009483992511 11.4009483992511 7.60152472832673e-07 0.000201506505515687
+ENSDARG00000099753 1 0.121501943616094 1.29493126702895 10.6577000210014 1.17807930734258e-06 0.000299281230702821
+ENSDARG00000076005 1 0.1 1.05371686166029 10.5371686166029 1.32743044013891e-06 0.00029931174491888
+ENSDARG00000041750 2 0.118845246250015 4.25427279350112 35.7967434772393 1.39550360463363e-07 0.000850838547745124
+ENSDARG00000103735 2 0.119337350478008 3.54379562135099 29.6956117020886 9.49083511390771e-07 0.00228722429441009
+ENSDARG00000101886 2 0.215092571957637 5.30165157388469 24.6482318084367 1.12541789129576e-06 0.00228722429441009
+ENSDARG00000090914 2 0.122178374276303 3.1027845112115 25.3955295246819 1.65948635889896e-06 0.00252947208255174
+ENSDARG00000090496 2 0.111721506487875 2.96053053983273 26.4991999562235 2.19562316256802e-06 0.00267734288443544
+ENSDARG00000078308 2 0.1 2.64934229048601 26.4934229048601 2.65009460603265e-06 0.00269293780216352
+ENSDARG00000075253 2 0.121220276605515 2.61038833734525 21.534254915456 7.21609407341446e-06 0.00624434487572006
+ENSDARG00000086877 2 0.174901657246515 3.44134351834849 19.6758771330457 8.19333426369698e-06 0.00624434487572006
+ENSDARG00000040487 2 0.132551316615554 2.19579056306671 16.5655884764638 5.8552609335758e-05 0.0389789127774957
+ENSDARG00000052912 2 0.29374667394921 3.98299817184644 13.5592962408661 6.97030598265265e-05 0.0389789127774957
+ENSDARG00000052558 2 0.307266492503596 4.25427279350112 13.8455474231422 7.0324428498024e-05 0.0389789127774957
+ENSDARG00000012071 2 0.137312605449286 2.19567880375095 15.9903658995232 8.47157718952949e-05 0.0419371525043834
+ENSDARG00000052515 2 0.142741634362038 2.26259398496241 15.8509743500887 8.94182356170222e-05 0.0419371525043834
+ENSDARG00000002897 2 0.155152648803008 2.06464107607378 13.3071597037005 0.000108713544348236 0.047344748563657
+ENSDARG00000087601 2 0.220544850783226 3.03609059600962 13.7663182124972 0.000128704633773863 0.0523141434746162
+ENSDARG00000020581 2 0.132645565796613 1.97090942840696 14.8584644844365 0.000140065988406919 0.0533738957073114
+ENSDARG00000005368 2 0.109588039327212 1.71813717094559 15.6781450009842 0.000165794148578122 0.0594615837576948
+ENSDARG00000013006 2 0.139223723099655 1.9643911375366 14.1096006758166 0.000196735880595178 0.0666388146660444
+ENSDARG00000059690 2 0.220277183931972 2.42251643631602 10.9975821965482 0.000320441653294837 0.102828040007296
+ENSDARG00000007906 2 0.161941295286845 1.92988721804511 11.9172025555725 0.000357508658491656 0.108986514541181
+ENSDARG00000099235 2 0.355572431070773 3.47503570154998 9.77307405719064 0.0005137976966319 0.145982086583318
+ENSDARG00000058248 2 0.187973361461239 1.79476640836755 9.54798272699739 0.000556896211693426 0.145982086583318
+ENSDARG00000013168 2 0.122745621089648 1.36391188645772 11.1116948559948 0.000584796437234187 0.145982086583318
+ENSDARG00000089066 2 0.213734450098499 2.20785246938186 10.3298858390137 0.000627746814730416 0.145982086583318
+ENSDARG00000018559 2 0.216649831175799 2.21719732132153 10.2340136121426 0.000632257513971329 0.145982086583318
+ENSDARG00000108459 3 0.1 40.0486298308386 400.486298308386 1.17120842343972e-21 7.140857757712e-18
+ENSDARG00000106631 3 0.1 16.7209600896533 167.209600896533 1.27082371024938e-20 2.65261585580336e-17
+ENSDARG00000106893 3 0.109440335656379 20.3249081306309 185.716792704722 1.30520708010662e-20 2.65261585580336e-17
+ENSDARG00000106328 3 0.109440335656379 13.3207925346078 121.717394731248 1.812771473855e-19 2.76311691902349e-16
+ENSDARG00000107500 3 0.194403356563789 23.5777850278158 121.282808304183 8.16923386605951e-19 9.96156377627297e-16
+ENSDARG00000107098 3 0.407548050942585 20.6628907529452 50.7005019534645 7.91289296843658e-15 8.0408180714263e-12
+ENSDARG00000106626 3 0.322331939034494 11.7938446379915 36.5891281928763 3.19108227960682e-14 2.77943266553754e-11
+ENSDARG00000063254 3 0.1 1.54154831743065 15.4154831743065 6.16683050966547e-09 4.69989570217879e-06
+ENSDARG00000105532 3 0.1 1.2691654791726 12.691654791726 6.59753120473869e-08 4.46946086169909e-05
+ENSDARG00000102291 3 0.1 1.20003533117234 12.0003533117234 1.03313712547645e-07 6.29903705402992e-05
+ENSDARG00000098646 3 0.1 1.22194683967797 12.2194683967797 1.14432499391301e-07 6.3426813526251e-05
+ENSDARG00000096706 3 0.1 1.2471262087964 12.471262087964 1.27992769850814e-07 6.50309931483676e-05
+ENSDARG00000056322 3 0.1 1.15253315794626 11.5253315794626 1.81837361851978e-07 7.7399961295303e-05
+ENSDARG00000087417 3 0.1 1.1540362057603 11.540362057603 1.83177220114043e-07 7.7399961295303e-05
+ENSDARG00000100789 3 0.109440335656379 1.31018291186832 11.9716638660726 1.90421423557413e-07 7.7399961295303e-05
+ENSDARG00000076768 3 0.1 1.18681657849799 11.8681657849799 2.13741147520963e-07 8.1448736027207e-05
+ENSDARG00000091869 3 0.1 1.10007995897679 11.0007995897679 3.18290687070941e-07 0.000107899200006755
+ENSDARG00000101145 3 0.1 1.10059661347904 11.0059661347904 3.19125599577782e-07 0.000107899200006755
+ENSDARG00000091967 3 0.1 1.1236667156373 11.236667156373 3.57604258883062e-07 0.000107899200006755
+ENSDARG00000099207 3 0.1 1.13395237668583 11.3395237668583 3.75510462080806e-07 0.000107899200006755
+ENSDARG00000079762 3 0.1 1.13482318163712 11.3482318163712 3.77047564405683e-07 0.000107899200006755
+ENSDARG00000100342 3 0.118880671312758 1.11971099812246 9.4187809149955 3.89336132548567e-07 0.000107899200006755
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+ENSDARG00000101776 3 0.1 1.03711906765213 10.3711906765213 5.36963212129621e-07 0.000136411029348096
+ENSDARG00000077068 3 0.1 1.0531104586081 10.531104586081 5.84457768774286e-07 0.000138268351040062
+ENSDARG00000103380 4 0.118732364944267 4.29504915730337 36.1742070859909 1.87281976492061e-10 1.1418582106721e-06
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+ENSDARG00000102060 4 0.65335417049578 14.8778451385581 22.7714856817527 8.75163683692952e-09 1.77862432649198e-05
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+ENSDARG00000101413 4 0.163690456191388 2.80861987923491 17.1581162676402 3.73531302510856e-07 0.000379570058568115
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+ENSDARG00000102705 5 0.209972550128478 13.5265663218744 64.4206412390466 5.51324807068058e-17 3.36142734869395e-13
+ENSDARG00000102125 5 0.233431470953978 10.4713938457086 44.8585351534415 1.77193932024865e-15 5.401757017778e-12
+ENSDARG00000105858 5 0.462925527809972 31.4875823414393 68.0186778430692 3.07338903352449e-15 6.24615097913294e-12
+ENSDARG00000104031 5 0.417738843341455 16.1643635536032 38.6949018777042 4.63887116279502e-14 7.07079936989031e-11
+ENSDARG00000103505 5 0.455814556718891 13.0057940562389 28.5330818521002 8.00401069394782e-13 8.56538424116237e-10
+ENSDARG00000107953 5 0.768435533248605 31.7530045869607 41.3216245385258 8.42911357175237e-13 8.56538424116237e-10
+ENSDARG00000104624 5 0.586363931713224 18.662951819579 31.8282738930583 1.03929690687218e-12 9.05227605885665e-10
+ENSDARG00000107433 5 0.860111367092678 34.1815671825659 39.7408620445342 2.15526546944614e-12 1.64258169590164e-09
+ENSDARG00000105003 5 0.659817827005108 18.3691699000608 27.8397599280362 4.05465742511909e-12 2.74680514677235e-09
+ENSDARG00000102147 5 0.498991534801074 11.6870331272134 23.4213053972398 5.94420491301204e-12 3.62418173546344e-09
+ENSDARG00000104149 5 0.591410894158957 12.7563563319083 21.5693631245145 2.16849130014449e-11 1.20193558699827e-08
+ENSDARG00000105370 5 0.845960751451064 21.1606791594491 25.0137835864755 2.88314145770954e-11 1.46487612230459e-08
+ENSDARG00000102471 5 0.591016786322552 11.9787944006235 20.2681119687961 3.97757415291587e-11 1.86548227771754e-08
+ENSDARG00000104225 5 0.677500552858849 13.028628755702 19.2304326553315 8.48219367396283e-11 3.69399534501081e-08
+ENSDARG00000102765 5 0.710420955035912 7.69305581025659 10.8288694973358 2.636812754442e-08 1.07177649092219e-05
+ENSDARG00000103900 5 0.926463189872816 8.83493365876684 9.53619502139064 1.4891189989945e-07 5.67447408554341e-05
+ENSDARG00000103207 5 0.809155048654974 6.95078624248591 8.5901784262978 3.17107715066467e-07 0.000113729749338838
+ENSDARG00000100850 5 0.10266571617904 1.06794343733293 10.4021427705286 3.65574205111742e-07 0.000123828107142572
+ENSDARG00000100222 5 0.117813108572049 1.02376729835175 8.6897571141302 1.53996760366899e-06 0.000376422800056221
+ENSDARG00000078327 5 0.105063152860082 0.901542752536163 8.58096038424425 1.59754149266682e-06 0.000376422800056221
+ENSDARG00000076659 5 0.107997148537119 0.902203678729055 8.35395833084392 1.63475485205548e-06 0.000376422800056221
+ENSDARG00000078658 5 0.103730294770562 0.912796947051807 8.79971419218265 1.70133206806343e-06 0.000376422800056221
+ENSDARG00000056152 5 0.109363711084075 0.821293559013241 7.50974478528675 2.30482270129059e-06 0.000411281146237518
+ENSDARG00000042974 5 0.111761147765118 0.823872029464418 7.37172126395753 2.39063753034635e-06 0.000411281146237518
+ENSDARG00000071240 5 0.110394585218162 0.833280258058883 7.54819864046915 2.53282560651987e-06 0.000411281146237518
+ENSDARG00000094010 6 0.111452978443105 4.44006630603854 39.8380228869803 6.38525950158321e-09 3.89309271811528e-05
+ENSDARG00000103594 6 1.13093354481739 15.5296459037369 13.7317050810836 2.76457859470178e-05 0.0842781784594839
+ENSDARG00000062868 6 0.148310913360651 2.35945460562356 15.9088400992179 4.74734577891717e-05 0.0964818907135266
+ENSDARG00000101986 6 1.06278096568171 11.921270245687 11.2170528365083 0.000104992972874659 0.160035538904199
+ENSDARG00000054302 6 0.114167149192999 1.69385093295239 14.8365878006548 0.000159146295603994 0.194062992859511
+ENSDARG00000004931 6 0.146147835707832 1.50738986001055 10.3141442547532 0.000273967771010734 0.271604620436783
+ENSDARG00000099280 6 0.174438502158969 1.76393397177854 10.1120678631546 0.000341416753578639 0.271604620436783
+ENSDARG00000104949 6 1.84012138595949 18.1422310489148 9.85925775731088 0.000356378048793549 0.271604620436783
+ENSDARG00000062192 6 0.219250133212514 1.93124420721189 8.8084060835666 0.000490459989622772 0.332259395192227
+ENSDARG00000014366 6 0.135611988044807 1.00529217065682 7.41300371118129 0.00101799998551309 0.595386680453464
+ENSDARG00000099776 6 0.165584080167415 1.27670227417667 7.7102960193145 0.00113607374054731 0.595386680453464
+ENSDARG00000014017 6 0.130935742022126 1.13118855425646 8.63926485455216 0.00124672027506227 0.595386680453464
+ENSDARG00000004527 6 0.161768890546368 1.40411105178857 8.67973469463903 0.00130573477419644 0.595386680453464
+ENSDARG00000015851 6 0.211160123828113 1.42542261170536 6.75043462687903 0.00136713359461186 0.595386680453464
+ENSDARG00000017037 6 0.11090453956233 0.860975851160853 7.76321559566973 0.0016197152098211 0.658360242285282
+ENSDARG00000018146 6 0.124837526779085 0.822444876257476 6.58812215747347 0.00208359331018621 0.755769031195207
+ENSDARG00000094732 6 0.201066488547157 1.22521720805992 6.09359230826055 0.00228107117057515 0.755769031195207
+ENSDARG00000021855 6 0.109168767482819 1.07499270061704 9.84707188149048 0.00231989733905826 0.755769031195207
+ENSDARG00000062058 6 0.122552380041629 0.881708382142295 7.19454311570935 0.00235519297895833 0.755769031195207
+ENSDARG00000089032 6 0.150988259365316 1.23158448554809 8.15682285977133 0.00250441767427358 0.7634717280023
+ENSDARG000001032071 6 1.66376642491526 10.8791567395556 6.53887263057956 0.00264170112721662 0.766973893935226
+ENSDARG00000101652 6 0.117661697666601 1.00798229432208 8.5667835354393 0.00288382859301584 0.79921376961898
+ENSDARG00000036809 6 0.178132306667668 1.05062387043439 5.89799733742001 0.0033324167246799 0.875163147449564
+ENSDARG00000037018 6 0.13196794390221 0.929979569662069 7.04701113136379 0.00344495908459727 0.875163147449564
+ENSDARG00000077737 6 0.229953264257691 1.41304633493481 6.1449283596658 0.00500781997902645 1
+ENSDARG00000104242 7 0.447206731128574 14.3756294075549 32.1453779805067 2.30113131457065e-13 1.40299976249373e-09
+ENSDARG00000102056 7 0.463880684093747 12.1589657830654 26.2114078037536 2.08698751307313e-12 6.36218143360344e-09
+ENSDARG00000102470 7 0.825035359668146 13.4793918534294 16.3379565438882 1.10737149331994e-09 2.25054799825723e-06
+ENSDARG00000104836 7 1.0201341649907 17.1513950198419 16.8128816860067 1.79596375972667e-09 2.73749776076337e-06
+ENSDARG00000104197 7 0.868813330133413 13.2077072533743 15.2020080669644 2.27590161725937e-09 2.77523443208607e-06
+ENSDARG00000102167 7 0.911623267267556 12.5281341487954 13.7426660755889 6.03157787269791e-09 6.12908838163986e-06
+ENSDARG00000105195 7 1.35837446108669 20.6382812121625 15.193366632977 1.20671859497662e-08 1.05105189622463e-05
+ENSDARG00000105669 7 1.55320812115904 19.4772872937536 12.5400369908053 8.3653757257818e-08 6.37546197501146e-05
+ENSDARG00000102820 7 1.12752840077096 11.8419301998565 10.5025560258699 1.31966552783421e-07 8.94000080356132e-05
+ENSDARG00000092989 7 0.133042434280628 1.21637077531351 9.14272789648302 2.82608004083509e-07 0.000172306100089716
+ENSDARG00000061806 7 0.13278988077121 1.12194957012091 8.44905924762421 7.25529240779189e-07 0.000402141071002793
+ENSDARG00000095512 7 0.134733887854507 1.08703031970933 8.06798005326739 1.27119959332606e-06 0.000645875326709081
+ENSDARG00000090634 7 0.14895440642195 1.13152352961684 7.5964421382173 1.67131715307221e-06 0.000689864250270158
+ENSDARG00000087555 7 0.106854974051793 0.876076138239269 8.19873989033614 1.8103703467808e-06 0.000689864250270158
+ENSDARG00000069269 7 0.131991994835001 1.03283452343888 7.82497851274993 2.01967640768832e-06 0.000724351003392688
+ENSDARG00000059558 7 0.112699471961133 0.967793901919788 8.58738630340302 3.00038333622434e-06 0.000888688802910736
+ENSDARG00000060566 7 0.127846770606366 1.01035836252462 7.90288528785342 3.78083155119976e-06 0.000992894397782283
+ENSDARG00000100206 7 0.139832328948304 1.04998427596811 7.5088806992286 4.54325865418129e-06 0.000992894397782283
+ENSDARG00000057206 7 0.121885624201679 0.88338782626096 7.24767856789453 4.55979057534917e-06 0.000992894397782283
+ENSDARG00000070623 7 0.12670584582223 0.943766658477006 7.44848552450473 5.87432370429556e-06 0.00110819712277626
+ENSDARG00000100514 7 0.121454028840368 0.820406006163069 6.75486860334098 7.45177975757828e-06 0.00116897636495374
+ENSDARG00000039265 7 0.131635113592875 0.87126351316452 6.6187773868543 9.18440046329954e-06 0.00133326880058898
+ENSDARG00000095904 7 0.168129332968718 1.08581712830248 6.45822539785194 1.03525068635208e-05 0.00139894259529663
+ENSDARG00000039350 7 0.133011711683714 0.897490439418404 6.74745425088979 1.06942592337219e-05 0.00139894259529663
+ENSDARG00000070512 7 0.12670239660567 0.910072943888678 7.18276029711621 1.10515908767776e-05 0.00139894259529663
+ENSDARG00000103551 8 1.61835767565622 32.2654393890171 19.93714978732 1.97522608849965e-06 0.0120429534615824
+ENSDARG00000078383 8 0.182610070366458 2.60621132144157 14.2720021749703 1.6366673021414e-05 0.0447464228757837
+ENSDARG00000093799 8 0.115321017732354 1.62941087246693 14.1293487042283 2.20172656433248e-05 0.0447464228757837
+ENSDARG00000036625 8 0.119337255991682 1.48171990557204 12.4162391137543 8.39663841121717e-05 0.127985760982978
+ENSDARG00000016706 8 0.180025642511508 1.82486224560436 10.1366795315712 0.000126325160000158 0.154040900104192
+ENSDARG00000040251 8 0.121540951107174 1.29918699186992 10.6892942669529 0.000198034398721646 0.201235954834313
+ENSDARG00000098674 8 0.253812764860557 2.21906493621457 8.74292093793513 0.000293366486612692 0.255522209839655
+ENSDARG00000098856 8 0.194513509828675 1.64663383642527 8.46539573459756 0.000451769293400039 0.296721325111977
+ENSDARG00000062226 8 0.144813536626749 1.38335068305012 9.55263378875725 0.000474939776632199 0.296721325111977
+ENSDARG00000075123 8 0.142439266402834 1.40532056857682 9.86610366696508 0.00048666774661633 0.296721325111977
+ENSDARG00000070239 8 0.154515334275144 1.27289156626506 8.23796273836765 0.000570475520527726 0.316199022605232
+ENSDARG00000026180 8 0.151758427938041 1.41564289946672 9.32826544595394 0.000683459166751383 0.347254211640265
+ENSDARG00000104786 8 0.182483274181232 1.61787042996763 8.8658559927024 0.00078762411588287 0.369395710349066
+ENSDARG00000101061 8 0.255483815147335 1.62613690189592 6.36493118344166 0.00150635451453941 0.61883047685698
+ENSDARG00000016584 8 0.135272462199637 0.880366460381022 6.50809814551733 0.00158197684628705 0.61883047685698
+ENSDARG00000070256 8 0.203213690445973 1.26976802854965 6.24843742448165 0.00178015471505539 0.61883047685698
+ENSDARG00000062745 8 0.130428963634169 0.955091918456498 7.32269805604966 0.00182445112094621 0.61883047685698
+ENSDARG00000086037 8 0.19632007891506 1.29918699186992 6.61769799120764 0.00182695564760138 0.61883047685698
+ENSDARG00000027310 8 0.193675103177481 1.44901164174846 7.48166190685131 0.00211840042255122 0.678671506770642
+ENSDARG00000103109 8 0.14293938597264 0.936026560054929 6.54841598545899 0.00240745117064372 0.678671506770642
+ENSDARG00000078352 8 0.177346649454539 1.15788746142844 6.52895030715114 0.0024876207141355 0.678671506770642
+ENSDARG00000035389 8 0.143574445102194 1.00421593036345 6.99439186164828 0.0026995869399452 0.678671506770642
+ENSDARG00000103106 8 0.175526172559138 1.23041862190788 7.00988692437495 0.0027017171947583 0.678671506770642
+ENSDARG00000007257 8 0.157933075856061 0.866671316548008 5.48758587680447 0.0028384639169755 0.678671506770642
+ENSDARG00000010596 8 0.110516369140454 0.836156159426777 7.56590327686312 0.00297745919336174 0.678671506770642
diff -r 000000000000 -r ff7cd3c7c1df test-data/intestinal.pdf
Binary file test-data/intestinal.pdf has changed
diff -r 000000000000 -r ff7cd3c7c1df test-data/intestinal_advanced.filter.pdf
Binary file test-data/intestinal_advanced.filter.pdf has changed
diff -r 000000000000 -r ff7cd3c7c1df test-data/intestinal_advanced.genelist
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/intestinal_advanced.genelist Thu Nov 22 04:43:00 2018 -0500
@@ -0,0 +1,251 @@
+n mean.ncl mean.cl fc pv padj
+ENSDARG00000109030 1 0.274654337828615 39.4233419769949 143.538027794031 1.85453080866619e-17 1.13070743404378e-13
+ENSDARG00000108798 1 0.327573035068885 24.802335939268 75.7154383420246 1.23506199101042e-15 3.76508647959528e-12
+ENSDARG00000107599 1 0.564182966938587 21.783984071531 38.6115592779005 1.43241168538371e-12 2.9111380152615e-09
+ENSDARG00000108379 1 0.68986839145523 24.7427021224644 35.8658295247755 7.59420613442267e-12 1.15754687003938e-08
+ENSDARG00000107321 1 0.1 2.23096784138222 22.3096784138222 6.33189194610656e-10 7.72110903908234e-07
+ENSDARG00000105564 1 0.1 1.97081703295526 19.7081703295526 2.35709418427607e-09 2.3952005402552e-06
+ENSDARG00000107138 1 0.12141391587535 1.84891204400927 15.22817241071 3.76162108069457e-08 3.27637196128497e-05
+ENSDARG00000105857 1 0.105759843800846 1.57285911501407 14.8719878782715 1.52193964569649e-07 0.000115990825247643
+ENSDARG00000090447 1 0.117044445524061 1.5247401265198 13.0270182381816 2.86307072797404e-07 0.000193957135871753
+ENSDARG00000068650 1 0.118444706911236 1.42924397145598 12.0667610121833 4.76963874982118e-07 0.000290804874576597
+ENSDARG00000029234 1 0.107704361452076 1.2680785099502 11.7736969316181 7.26433141517866e-07 0.000402642078530403
+ENSDARG00000100003 1 0.120259003658528 1.3511174001475 11.2350623158659 8.51760668849063e-07 0.000432765399831061
+ENSDARG00000105009 1 0.114133477721009 1.43604387395694 12.5821441931984 1.07513161417496e-06 0.000468412297206485
+ENSDARG00000104049 1 0.14589886302348 1.5016492143503 10.2923983314978 1.07557358715611e-06 0.000468412297206485
+ENSDARG00000031751 1 0.1 1.1027874555083 11.027874555083 1.18468481582687e-06 0.000481534888139762
+ENSDARG00000061520 1 0.112439513940038 1.16615674720545 10.371413983765 1.26583755719038e-06 0.000482363224136858
+ENSDARG00000069937 1 0.106429116268933 1.19711464307861 11.2479994671162 1.3914597563853e-06 0.000489927544230463
+ENSDARG00000102310 1 0.171334245177586 1.69584918039039 9.89789973763077 1.44639917929282e-06 0.000489927544230463
+ENSDARG00000070971 1 0.105759843800846 1.23615093236413 11.6882825081691 1.59484544299157e-06 0.000511777508732612
+ENSDARG00000059700 1 0.123792889999442 1.30060829013998 10.5063246374314 1.70455892742405e-06 0.000519634789025223
+ENSDARG00000105822 1 0.116254840089654 1.36190382019475 11.7148139307101 2.0009977480624e-06 0.000580956346187449
+ENSDARG00000006900 1 0.112188960069779 1.0855926347724 9.67646579571808 2.38826556387865e-06 0.000596724400597127
+ENSDARG00000107086 1 0.206384379895952 1.78478473504023 8.64786732377724 2.51061474571093e-06 0.000596724400597127
+ENSDARG00000053609 1 0.118868630208971 1.19424467810985 10.0467606635188 2.82886104616545e-06 0.000596724400597127
+ENSDARG00000074906 1 0.107949710622428 1.13463616544336 10.5107846876213 2.85219448553942e-06 0.000596724400597127
+ENSDARG00000103380 2 0.11744425852746 2.69709661708924 22.9649082118273 3.51926611140710e-10 2.14569654812491e-06
+ENSDARG00000063254 2 0.111022543280608 2.02476739062929 18.2374437731238 3.47469814170424e-09 1.05926172849854e-05
+ENSDARG00000037116 2 0.141198375384836 1.87841400172861 13.3033683752309 1.69857431590056e-07 0.000345206920134858
+ENSDARG00000041750 2 0.117649821642336 1.39900877363844 11.8912953212248 9.77345771313156e-07 0.00148971929192408
+ENSDARG00000098655 2 0.141845782279186 1.57030807712408 11.0705306276457 1.26469583240448e-06 0.00154217009803402
+ENSDARG00000043130 2 0.134744785219575 1.37280311614026 10.1881725062918 1.81996279029707e-06 0.00164994216311116
+ENSDARG00000041060 2 0.147891926689861 1.43420850443861 9.69767949163475 1.89430787957653e-06 0.00164994216311116
+ENSDARG00000055855 2 0.1 1.02997101954978 10.2997101954978 2.42199148547504e-06 0.00184586026086767
+ENSDARG00000071113 2 0.118763752041103 1.2047658368423 10.1442217523183 2.9327526474996e-06 0.00198677698797834
+ENSDARG00000103735 2 0.118194651323328 1.18040041297686 9.98691903365242 6.64944770047414e-06 0.00405416826297908
+ENSDARG00000101886 2 0.209743544174361 1.81475059822713 8.65223578332648 7.34189530589232e-06 0.00406941233454777
+ENSDARG00000090914 2 0.12455462866305 1.02393369575738 8.22075989265215 9.97355487382862e-06 0.00431922830390302
+ENSDARG00000070155 2 0.145636384675691 1.22381003950119 8.4031888200632 1.10995775094098e-05 0.00431922830390302
+ENSDARG00000078308 2 0.1 0.884413012457234 8.84413012457234 1.11052707489314e-05 0.00431922830390302
+ENSDARG00000055075 2 0.140874517470988 1.23123837236169 8.73996514391085 1.11859975284501e-05 0.00431922830390302
+ENSDARG00000075333 2 0.173616356090642 1.49236455140212 8.59576012886123 1.13346978616448e-05 0.00431922830390302
+ENSDARG00000090496 2 0.109762824048538 1.00093423404816 9.11906415240863 1.26126603603098e-05 0.00452349354216524
+ENSDARG00000102171 2 0.20167547700855 1.51293988351994 7.50185350227681 1.6095088472438e-05 0.00545176413424746
+ENSDARG00000005606 2 0.1 0.836321702997769 8.36321702997769 2.84519645106893e-05 0.00913008566429856
+ENSDARG00000103046 2 0.15133579690267 1.20330527846178 7.95122702684595 4.04140901343646e-05 0.0123202353774611
+ENSDARG00000075253 2 0.120279319535925 0.893198171744321 7.42603279757947 4.39003628324243e-05 0.0127457386756805
+ENSDARG00000012946 2 0.171826008980895 1.14690599580048 6.67481019085999 5.87419981139685e-05 0.0162795437500394
+ENSDARG00000004726 2 0.204332888209134 1.32511161300844 6.48506280424223 7.83412783189708e-05 0.0200555134502627
+ENSDARG00000099280 2 0.138586053017945 1.01744489261619 7.341611009619 7.89457639505174e-05 0.0200555134502627
+ENSDARG00000007906 2 0.130359275171119 0.909993093806384 6.98065475288859 8.37456466719854e-05 0.0204238883103638
+ENSDARG00000105948 3 0.124767865711445 1.62656171856877 13.0367038763857 2.61168950906914e-06 0.00703175443956562
+ENSDARG00000055722 3 0.170883221228216 2.00283737635957 11.720503405567 3.95089635339007e-06 0.00703175443956562
+ENSDARG00000106893 3 1.82739874604305 23.7425603573802 12.9925449542915 4.57452266266905e-06 0.00703175443956562
+ENSDARG00000061718 3 0.137307773346157 1.62578493731802 11.8404435357012 4.61325533184558e-06 0.00703175443956562
+ENSDARG00000106328 3 1.39137546603467 13.9976679031936 10.0603095604999 1.42962408910711e-05 0.0168948038256923
+ENSDARG00000102647 3 0.129955363360119 1.24434788249555 9.57519451542249 1.87312904978666e-05 0.0168948038256923
+ENSDARG00000074790 3 0.127809562649142 1.26033195054844 9.86101450020806 1.9397019317672e-05 0.0168948038256923
+ENSDARG00000105532 3 0.18700466476476 1.58761868064531 8.48972769017518 2.91879023278545e-05 0.0196404362687073
+ENSDARG00000076801 3 0.184104189252268 1.69805549674687 9.22333980363762 3.4509692498395e-05 0.0196404362687073
+ENSDARG00000094709 3 0.169002302456185 1.52988725489916 9.05246397631649 3.75963772768908e-05 0.0196404362687073
+ENSDARG00000106626 3 1.42200147747789 12.5130329610575 8.79959209553782 3.83265050783588e-05 0.0196404362687073
+ENSDARG00000060741 3 0.130268153184582 1.12645607566602 8.64720999053316 3.86559349228288e-05 0.0196404362687073
+ENSDARG00000091631 3 0.161325472723805 1.36766090797707 8.47765008764954 4.18818834282309e-05 0.0196426033278403
+ENSDARG00000029501 3 0.153557572558019 1.47164556559853 9.58367302297968 5.01571281004926e-05 0.0218434292877645
+ENSDARG00000106631 3 1.85932824529968 16.1395995585986 8.68033904147855 6.87495326958489e-05 0.0279443933897727
+ENSDARG00000075347 3 0.133792214183597 1.1967893889796 8.94513478442996 7.43716893706407e-05 0.0283402618807998
+ENSDARG00000076763 3 0.163861414003921 1.26230839743879 7.70351217284496 8.25394438939219e-05 0.0296025287894848
+ENSDARG00000054560 3 0.130018404596429 1.05134828356091 8.08614970183833 9.28265359870164e-05 0.0298309404950185
+ENSDARG00000063197 3 0.15690277178598 1.3288503204811 8.46925969092308 9.29617630646796e-05 0.0298309404950185
+ENSDARG00000076499 3 0.15722155193569 1.36893401320963 8.70703791150451 0.000100100169269367 0.0305155366017665
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+ENSDARG00000017093 9 0.136411665631298 1.61606550277123 11.8469743426433 0.00134953377699747 0.357743801667547
+ENSDARG00000075292 9 0.270507213308798 2.1951121474112 8.11480078686617 0.00167879474511109 0.409991689104941
+ENSDARG00000057011 9 0.145230732286546 1.55832371169181 10.7299859138434 0.00168112058842439 0.409991689104941
+ENSDARG00000101413 10 0.141224429692467 1.80827014074558 12.8042304343753 1.53774069797456e-07 0.000937560503555091
+ENSDARG00000069269 10 0.136680427340329 1.39111418584467 10.177859499816 7.9409154224428e-07 0.00242078806653169
+ENSDARG00000096457 10 0.108692378208486 0.98849791094733 9.09445471007417 8.01600268921674e-06 0.0136362534840021
+ENSDARG00000058178 10 0.135168786411076 1.1479669345012 8.49284043292363 8.94620533639631e-06 0.0136362534840021
+ENSDARG000001048361 10 2.19609208044308 17.0930420303104 7.78339040631744 2.81321418960958e-05 0.0308316937773483
+ENSDARG00000093313 10 0.126396920024548 0.901779535343549 7.13450561270331 3.03411780652928e-05 0.0308316937773483
+ENSDARG00000040705 10 0.156669586745304 1.04105796280058 6.64492697292305 4.60453020521687e-05 0.0389962833230328
+ENSDARG00000010270 10 0.125615247910794 0.792776147157419 6.31114582300081 5.11678311602858e-05 0.0389962833230328
+ENSDARG00000016348 10 0.141266983378295 1.03650793650794 7.33722708392734 6.15803180656218e-05 0.0391750861522631
+ENSDARG00000104197 10 1.88512035781081 12.4705558421044 6.61525710569826 6.81411845087847e-05 0.0391750861522631
+ENSDARG00000086471 10 0.185942018777691 1.10768386676327 5.95714660970523 7.06783578276028e-05 0.0391750861522631
+ENSDARG00000102820 10 1.91136642367287 11.7867769779747 6.16667575196038 0.000123177015995738 0.0494349967701024
+ENSDARG00000076025 10 0.1358413706015 0.865139546616693 6.36874865724554 0.000127769715977776 0.0494349967701024
+ENSDARG00000060566 10 0.175513373838258 1.10598275418622 6.30141584085455 0.000145658259770009 0.0494349967701024
+ENSDARG00000077760 10 0.172527864230777 0.981147246329388 5.68689150998233 0.000146283831624913 0.0494349967701024
+ENSDARG000001056691 10 2.91736340526917 19.0715434690697 6.53725327280921 0.000159343665923593 0.0494349967701024
+ENSDARG00000097110 10 0.207251034236892 1.10961177579611 5.35395048754164 0.00017068480864505 0.0494349967701024
+ENSDARG00000017127 10 0.321847124787121 1.71261097592378 5.32119395833208 0.000176225214760411 0.0494349967701024
+ENSDARG00000016138 10 0.150588587792026 0.814494514984075 5.40873997775283 0.00018078366550766 0.0494349967701024
+ENSDARG00000057568 10 0.149007737391486 0.825280606125021 5.53850840615591 0.00018777552481366 0.0494349967701024
+ENSDARG000001042421 10 1.9682001003536 11.3276355799035 5.7553272037068 0.000196708249110425 0.0494349967701024
+ENSDARG00000018593 10 0.167994135041575 0.898088080558678 5.34594901385347 0.000257112102487736 0.0529172584853715
+ENSDARG00000057206 10 0.170963878363685 0.918781977468761 5.37412923865865 0.000277735324181054 0.0529172584853715
+ENSDARG000001051951 10 3.11026247187605 18.5149051843724 5.95284332167778 0.000320190438588827 0.0533324207357922
+ENSDARG00000079934 10 0.198961295595687 1.08503079710172 5.45347673703652 0.00032037005450948 0.0533324207357922
diff -r 000000000000 -r ff7cd3c7c1df test-data/intestinal_advanced.pdf
Binary file test-data/intestinal_advanced.pdf has changed
diff -r 000000000000 -r ff7cd3c7c1df test-data/matrix.filter.pdf
Binary file test-data/matrix.filter.pdf has changed
diff -r 000000000000 -r ff7cd3c7c1df test-data/matrix.filter.rdat
Binary file test-data/matrix.filter.rdat has changed
diff -r 000000000000 -r ff7cd3c7c1df test-data/matrix.genelist
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/matrix.genelist Thu Nov 22 04:43:00 2018 -0500
@@ -0,0 +1,201 @@
+n mean.ncl mean.cl fc pv padj
+ENSDARG00000108798 1 0.13225291542414 22.6067842060994 170.935998904815 5.63439752001819e-20 3.43529216795509e-16
+ENSDARG00000109030 1 0.186711263967539 34.6842724288799 185.764220603798 2.48233981248329e-19 7.56741291835532e-16
+ENSDARG00000108379 1 0.168199368419563 24.3874482842581 144.991319012715 4.11994031997326e-19 8.37309204362565e-16
+ENSDARG00000107599 1 0.194980763882093 20.9729826342942 107.564367975175 3.56470297051077e-18 5.43349850280104e-15
+ENSDARG00000107321 1 0.1 1.94683879586459 19.4683879586459 1.39905888784068e-09 1.70601240783292e-06
+ENSDARG00000105564 1 0.1 1.72137476189456 17.2137476189456 5.11677986670882e-09 5.19950114122061e-06
+ENSDARG00000090447 1 0.1 1.4302236712519 14.302236712519 3.51620742912878e-08 3.06261667077116e-05
+ENSDARG00000079591 1 0.11578454541401 1.47825950354764 12.767330028907 4.83701028926633e-08 3.6864064667071e-05
+ENSDARG00000107138 1 0.118643244515052 1.63372529702772 13.7700659123533 8.59237265783686e-08 5.36793599520202e-05
+ENSDARG00000041060 1 0.11578454541401 1.4382199783801 12.421519411226 8.84781911763433e-08 5.36793599520202e-05
+ENSDARG00000077004 1 0.1 1.29299827494356 12.9299827494356 1.0364347799037e-07 5.36793599520202e-05
+ENSDARG00000100003 1 0.1 1.29775216728225 12.9775216728225 1.05650700249999e-07 5.36793599520202e-05
+ENSDARG00000102310 1 0.129577145917004 1.72085266498654 13.2805260743185 1.20446928962954e-07 5.64896096836256e-05
+ENSDARG00000068650 1 0.115601615820105 1.27001296748153 10.9861177845289 2.26895176903151e-07 9.88128495413223e-05
+ENSDARG00000086678 1 0.128030253978187 1.35647794130946 10.5949796955067 3.16910756640577e-07 0.000122948041506908
+ENSDARG00000105857 1 0.105900327795989 1.37647789967886 12.9978625026598 3.22645344285801e-07 0.000122948041506908
+ENSDARG00000105159 1 0.1 1.16700756453584 11.6700756453584 3.44329675018825e-07 0.000123492825211163
+ENSDARG00000102997 1 0.125930886410326 1.40950930054417 11.1927211879659 3.75314178672153e-07 0.00012712725263134
+ENSDARG00000052615 1 0.109701288024116 1.2495211865536 11.3902143635625 4.65728278602572e-07 0.000149449753402099
+ENSDARG00000103046 1 0.111800655591977 1.27916812008568 11.441508221151 5.24275745356588e-07 0.000158237500570989
+ENSDARG00000105009 1 0.107892272707005 1.29390774186871 11.9925895470056 5.45020093815115e-07 0.000158237500570989
+ENSDARG00000069937 1 0.1 1.08683574177416 10.8683574177416 5.98190849813324e-07 0.000165780436877811
+ENSDARG00000034941 1 0.1 1.14009483992511 11.4009483992511 7.60152472832673e-07 0.000201506505515687
+ENSDARG00000099753 1 0.121501943616094 1.29493126702895 10.6577000210014 1.17807930734258e-06 0.000299281230702821
+ENSDARG00000076005 1 0.1 1.05371686166029 10.5371686166029 1.32743044013891e-06 0.00029931174491888
+ENSDARG00000041750 2 0.118845246250015 4.25427279350112 35.7967434772393 1.39550360463363e-07 0.000850838547745124
+ENSDARG00000103735 2 0.119337350478008 3.54379562135099 29.6956117020886 9.49083511390771e-07 0.00228722429441009
+ENSDARG00000101886 2 0.215092571957637 5.30165157388469 24.6482318084367 1.12541789129576e-06 0.00228722429441009
+ENSDARG00000090914 2 0.122178374276303 3.1027845112115 25.3955295246819 1.65948635889896e-06 0.00252947208255174
+ENSDARG00000090496 2 0.111721506487875 2.96053053983273 26.4991999562235 2.19562316256802e-06 0.00267734288443544
+ENSDARG00000078308 2 0.1 2.64934229048601 26.4934229048601 2.65009460603265e-06 0.00269293780216352
+ENSDARG00000075253 2 0.121220276605515 2.61038833734525 21.534254915456 7.21609407341446e-06 0.00624434487572006
+ENSDARG00000086877 2 0.174901657246515 3.44134351834849 19.6758771330457 8.19333426369698e-06 0.00624434487572006
+ENSDARG00000040487 2 0.132551316615554 2.19579056306671 16.5655884764638 5.8552609335758e-05 0.0389789127774957
+ENSDARG00000052912 2 0.29374667394921 3.98299817184644 13.5592962408661 6.97030598265265e-05 0.0389789127774957
+ENSDARG00000052558 2 0.307266492503596 4.25427279350112 13.8455474231422 7.0324428498024e-05 0.0389789127774957
+ENSDARG00000012071 2 0.137312605449286 2.19567880375095 15.9903658995232 8.47157718952949e-05 0.0419371525043834
+ENSDARG00000052515 2 0.142741634362038 2.26259398496241 15.8509743500887 8.94182356170222e-05 0.0419371525043834
+ENSDARG00000002897 2 0.155152648803008 2.06464107607378 13.3071597037005 0.000108713544348236 0.047344748563657
+ENSDARG00000087601 2 0.220544850783226 3.03609059600962 13.7663182124972 0.000128704633773863 0.0523141434746162
+ENSDARG00000020581 2 0.132645565796613 1.97090942840696 14.8584644844365 0.000140065988406919 0.0533738957073114
+ENSDARG00000005368 2 0.109588039327212 1.71813717094559 15.6781450009842 0.000165794148578122 0.0594615837576948
+ENSDARG00000013006 2 0.139223723099655 1.9643911375366 14.1096006758166 0.000196735880595178 0.0666388146660444
+ENSDARG00000059690 2 0.220277183931972 2.42251643631602 10.9975821965482 0.000320441653294837 0.102828040007296
+ENSDARG00000007906 2 0.161941295286845 1.92988721804511 11.9172025555725 0.000357508658491656 0.108986514541181
+ENSDARG00000099235 2 0.355572431070773 3.47503570154998 9.77307405719064 0.0005137976966319 0.145982086583318
+ENSDARG00000058248 2 0.187973361461239 1.79476640836755 9.54798272699739 0.000556896211693426 0.145982086583318
+ENSDARG00000013168 2 0.122745621089648 1.36391188645772 11.1116948559948 0.000584796437234187 0.145982086583318
+ENSDARG00000089066 2 0.213734450098499 2.20785246938186 10.3298858390137 0.000627746814730416 0.145982086583318
+ENSDARG00000018559 2 0.216649831175799 2.21719732132153 10.2340136121426 0.000632257513971329 0.145982086583318
+ENSDARG00000108459 3 0.1 40.0486298308386 400.486298308386 1.17120842343972e-21 7.140857757712e-18
+ENSDARG00000106631 3 0.1 16.7209600896533 167.209600896533 1.27082371024938e-20 2.65261585580336e-17
+ENSDARG00000106893 3 0.109440335656379 20.3249081306309 185.716792704722 1.30520708010662e-20 2.65261585580336e-17
+ENSDARG00000106328 3 0.109440335656379 13.3207925346078 121.717394731248 1.812771473855e-19 2.76311691902349e-16
+ENSDARG00000107500 3 0.194403356563789 23.5777850278158 121.282808304183 8.16923386605951e-19 9.96156377627297e-16
+ENSDARG00000107098 3 0.407548050942585 20.6628907529452 50.7005019534645 7.91289296843658e-15 8.0408180714263e-12
+ENSDARG00000106626 3 0.322331939034494 11.7938446379915 36.5891281928763 3.19108227960682e-14 2.77943266553754e-11
+ENSDARG00000063254 3 0.1 1.54154831743065 15.4154831743065 6.16683050966547e-09 4.69989570217879e-06
+ENSDARG00000105532 3 0.1 1.2691654791726 12.691654791726 6.59753120473869e-08 4.46946086169909e-05
+ENSDARG00000102291 3 0.1 1.20003533117234 12.0003533117234 1.03313712547645e-07 6.29903705402992e-05
+ENSDARG00000098646 3 0.1 1.22194683967797 12.2194683967797 1.14432499391301e-07 6.3426813526251e-05
+ENSDARG00000096706 3 0.1 1.2471262087964 12.471262087964 1.27992769850814e-07 6.50309931483676e-05
+ENSDARG00000056322 3 0.1 1.15253315794626 11.5253315794626 1.81837361851978e-07 7.7399961295303e-05
+ENSDARG00000087417 3 0.1 1.1540362057603 11.540362057603 1.83177220114043e-07 7.7399961295303e-05
+ENSDARG00000100789 3 0.109440335656379 1.31018291186832 11.9716638660726 1.90421423557413e-07 7.7399961295303e-05
+ENSDARG00000076768 3 0.1 1.18681657849799 11.8681657849799 2.13741147520963e-07 8.1448736027207e-05
+ENSDARG00000091869 3 0.1 1.10007995897679 11.0007995897679 3.18290687070941e-07 0.000107899200006755
+ENSDARG00000101145 3 0.1 1.10059661347904 11.0059661347904 3.19125599577782e-07 0.000107899200006755
+ENSDARG00000091967 3 0.1 1.1236667156373 11.236667156373 3.57604258883062e-07 0.000107899200006755
+ENSDARG00000099207 3 0.1 1.13395237668583 11.3395237668583 3.75510462080806e-07 0.000107899200006755
+ENSDARG00000079762 3 0.1 1.13482318163712 11.3482318163712 3.77047564405683e-07 0.000107899200006755
+ENSDARG00000100342 3 0.118880671312758 1.11971099812246 9.4187809149955 3.89336132548567e-07 0.000107899200006755
+ENSDARG00000091631 3 0.1 1.0336438761938 10.336438761938 5.26923351033268e-07 0.000136411029348096
+ENSDARG00000101776 3 0.1 1.03711906765213 10.3711906765213 5.36963212129621e-07 0.000136411029348096
+ENSDARG00000077068 3 0.1 1.0531104586081 10.531104586081 5.84457768774286e-07 0.000138268351040062
+ENSDARG00000103380 4 0.118732364944267 4.29504915730337 36.1742070859909 1.87281976492061e-10 1.1418582106721e-06
+ENSDARG00000037116 4 0.105401803653084 3.3624106287092 31.9008832123606 6.24221125271845e-10 1.90293810039122e-06
+ENSDARG00000102060 4 0.65335417049578 14.8778451385581 22.7714856817527 8.75163683692952e-09 1.77862432649198e-05
+ENSDARG00000102188 4 0.855834419578633 14.179562474169 16.5681142868153 2.26488443176202e-07 0.000318621197056678
+ENSDARG00000105127 4 1.2186946752299 22.1380023868484 18.1653393887785 2.6129342058117e-07 0.000318621197056678
+ENSDARG00000101413 4 0.163690456191388 2.80861987923491 17.1581162676402 3.73531302510856e-07 0.000379570058568115
+ENSDARG00000104118 4 0.989700274307544 15.0174505397369 15.1737358567916 6.77423754716057e-07 0.000590036090357685
+ENSDARG00000075333 4 0.171748726689293 2.3373595505618 13.6091812476157 1.50828806455175e-06 0.00110856685474393
+ENSDARG00000071113 4 0.128246671314964 1.77801966292135 13.8640609123855 1.68613897165096e-06 0.00110856685474393
+ENSDARG00000098655 4 0.153148025950228 2.3373595505618 15.2620938863516 1.81821691773647e-06 0.00110856685474393
+ENSDARG00000105209 4 1.54534561735873 23.4939455347753 15.2030363116638 2.06788281463169e-06 0.00114617104734631
+ENSDARG00000092124 4 0.167783479025787 2.20080865760876 13.1169568683846 2.51104682731582e-06 0.00117801683762716
+ENSDARG00000102424 4 0.995458642689216 12.8896835165257 12.9484872236424 2.51176298001526e-06 0.00117801683762716
+ENSDARG00000043130 4 0.151115417204371 1.96446629213483 12.9997741360702 2.99111460631241e-06 0.00128615842311759
+ENSDARG00000102305 4 1.00227191359572 12.5079159542882 12.4795634643849 3.16424083102573e-06 0.00128615842311759
+ENSDARG00000104251 4 1.25657639483624 16.1896340694694 12.8839234415026 4.03444006517729e-06 0.00153737381733662
+ENSDARG00000016348 4 0.130718858025808 1.82528654590158 13.9634523546802 7.40568226139146e-06 0.00265602616162963
+ENSDARG00000107668 4 2.0525826270598 26.1651913798814 12.7474485240877 1.23716885008222e-05 0.00419056582163961
+ENSDARG00000102171 4 0.209616501874572 2.24413623595506 10.7059139709233 1.41333189895541e-05 0.0045353076778585
+ENSDARG00000102300 4 1.16111393148624 12.0981196442604 10.4194078773774 1.50789368610256e-05 0.00459681390208365
+ENSDARG00000096457 4 0.122651614608118 1.49305555555556 12.1731422804827 1.58593667087189e-05 0.00460450280109806
+ENSDARG00000102445 4 1.3115800466299 12.8389700502745 9.78893364782744 3.22055454104447e-05 0.00892532774397644
+ENSDARG00000089213 4 0.12779725761052 1.38681171572623 10.8516547354461 3.54676572069977e-05 0.00940201330395934
+ENSDARG00000105147 4 1.98689642082857 20.3540415496165 10.2441382128659 4.3971555566058e-05 0.0111706072619273
+ENSDARG00000055075 4 0.169741281332608 1.59157303370787 9.37646411770147 4.82148454826373e-05 0.0117586365163056
+ENSDARG00000102705 5 0.209972550128478 13.5265663218744 64.4206412390466 5.51324807068058e-17 3.36142734869395e-13
+ENSDARG00000102125 5 0.233431470953978 10.4713938457086 44.8585351534415 1.77193932024865e-15 5.401757017778e-12
+ENSDARG00000105858 5 0.462925527809972 31.4875823414393 68.0186778430692 3.07338903352449e-15 6.24615097913294e-12
+ENSDARG00000104031 5 0.417738843341455 16.1643635536032 38.6949018777042 4.63887116279502e-14 7.07079936989031e-11
+ENSDARG00000103505 5 0.455814556718891 13.0057940562389 28.5330818521002 8.00401069394782e-13 8.56538424116237e-10
+ENSDARG00000107953 5 0.768435533248605 31.7530045869607 41.3216245385258 8.42911357175237e-13 8.56538424116237e-10
+ENSDARG00000104624 5 0.586363931713224 18.662951819579 31.8282738930583 1.03929690687218e-12 9.05227605885665e-10
+ENSDARG00000107433 5 0.860111367092678 34.1815671825659 39.7408620445342 2.15526546944614e-12 1.64258169590164e-09
+ENSDARG00000105003 5 0.659817827005108 18.3691699000608 27.8397599280362 4.05465742511909e-12 2.74680514677235e-09
+ENSDARG00000102147 5 0.498991534801074 11.6870331272134 23.4213053972398 5.94420491301204e-12 3.62418173546344e-09
+ENSDARG00000104149 5 0.591410894158957 12.7563563319083 21.5693631245145 2.16849130014449e-11 1.20193558699827e-08
+ENSDARG00000105370 5 0.845960751451064 21.1606791594491 25.0137835864755 2.88314145770954e-11 1.46487612230459e-08
+ENSDARG00000102471 5 0.591016786322552 11.9787944006235 20.2681119687961 3.97757415291587e-11 1.86548227771754e-08
+ENSDARG00000104225 5 0.677500552858849 13.028628755702 19.2304326553315 8.48219367396283e-11 3.69399534501081e-08
+ENSDARG00000102765 5 0.710420955035912 7.69305581025659 10.8288694973358 2.636812754442e-08 1.07177649092219e-05
+ENSDARG00000103900 5 0.926463189872816 8.83493365876684 9.53619502139064 1.4891189989945e-07 5.67447408554341e-05
+ENSDARG00000103207 5 0.809155048654974 6.95078624248591 8.5901784262978 3.17107715066467e-07 0.000113729749338838
+ENSDARG00000100850 5 0.10266571617904 1.06794343733293 10.4021427705286 3.65574205111742e-07 0.000123828107142572
+ENSDARG00000100222 5 0.117813108572049 1.02376729835175 8.6897571141302 1.53996760366899e-06 0.000376422800056221
+ENSDARG00000078327 5 0.105063152860082 0.901542752536163 8.58096038424425 1.59754149266682e-06 0.000376422800056221
+ENSDARG00000076659 5 0.107997148537119 0.902203678729055 8.35395833084392 1.63475485205548e-06 0.000376422800056221
+ENSDARG00000078658 5 0.103730294770562 0.912796947051807 8.79971419218265 1.70133206806343e-06 0.000376422800056221
+ENSDARG00000056152 5 0.109363711084075 0.821293559013241 7.50974478528675 2.30482270129059e-06 0.000411281146237518
+ENSDARG00000042974 5 0.111761147765118 0.823872029464418 7.37172126395753 2.39063753034635e-06 0.000411281146237518
+ENSDARG00000071240 5 0.110394585218162 0.833280258058883 7.54819864046915 2.53282560651987e-06 0.000411281146237518
+ENSDARG00000094010 6 0.111452978443105 4.44006630603854 39.8380228869803 6.38525950158321e-09 3.89309271811528e-05
+ENSDARG00000103594 6 1.13093354481739 15.5296459037369 13.7317050810836 2.76457859470178e-05 0.0842781784594839
+ENSDARG00000062868 6 0.148310913360651 2.35945460562356 15.9088400992179 4.74734577891717e-05 0.0964818907135266
+ENSDARG00000101986 6 1.06278096568171 11.921270245687 11.2170528365083 0.000104992972874659 0.160035538904199
+ENSDARG00000054302 6 0.114167149192999 1.69385093295239 14.8365878006548 0.000159146295603994 0.194062992859511
+ENSDARG00000004931 6 0.146147835707832 1.50738986001055 10.3141442547532 0.000273967771010734 0.271604620436783
+ENSDARG00000099280 6 0.174438502158969 1.76393397177854 10.1120678631546 0.000341416753578639 0.271604620436783
+ENSDARG00000104949 6 1.84012138595949 18.1422310489148 9.85925775731088 0.000356378048793549 0.271604620436783
+ENSDARG00000062192 6 0.219250133212514 1.93124420721189 8.8084060835666 0.000490459989622772 0.332259395192227
+ENSDARG00000014366 6 0.135611988044807 1.00529217065682 7.41300371118129 0.00101799998551309 0.595386680453464
+ENSDARG00000099776 6 0.165584080167415 1.27670227417667 7.7102960193145 0.00113607374054731 0.595386680453464
+ENSDARG00000014017 6 0.130935742022126 1.13118855425646 8.63926485455216 0.00124672027506227 0.595386680453464
+ENSDARG00000004527 6 0.161768890546368 1.40411105178857 8.67973469463903 0.00130573477419644 0.595386680453464
+ENSDARG00000015851 6 0.211160123828113 1.42542261170536 6.75043462687903 0.00136713359461186 0.595386680453464
+ENSDARG00000017037 6 0.11090453956233 0.860975851160853 7.76321559566973 0.0016197152098211 0.658360242285282
+ENSDARG00000018146 6 0.124837526779085 0.822444876257476 6.58812215747347 0.00208359331018621 0.755769031195207
+ENSDARG00000094732 6 0.201066488547157 1.22521720805992 6.09359230826055 0.00228107117057515 0.755769031195207
+ENSDARG00000021855 6 0.109168767482819 1.07499270061704 9.84707188149048 0.00231989733905826 0.755769031195207
+ENSDARG00000062058 6 0.122552380041629 0.881708382142295 7.19454311570935 0.00235519297895833 0.755769031195207
+ENSDARG00000089032 6 0.150988259365316 1.23158448554809 8.15682285977133 0.00250441767427358 0.7634717280023
+ENSDARG000001032071 6 1.66376642491526 10.8791567395556 6.53887263057956 0.00264170112721662 0.766973893935226
+ENSDARG00000101652 6 0.117661697666601 1.00798229432208 8.5667835354393 0.00288382859301584 0.79921376961898
+ENSDARG00000036809 6 0.178132306667668 1.05062387043439 5.89799733742001 0.0033324167246799 0.875163147449564
+ENSDARG00000037018 6 0.13196794390221 0.929979569662069 7.04701113136379 0.00344495908459727 0.875163147449564
+ENSDARG00000077737 6 0.229953264257691 1.41304633493481 6.1449283596658 0.00500781997902645 1
+ENSDARG00000104242 7 0.447206731128574 14.3756294075549 32.1453779805067 2.30113131457065e-13 1.40299976249373e-09
+ENSDARG00000102056 7 0.463880684093747 12.1589657830654 26.2114078037536 2.08698751307313e-12 6.36218143360344e-09
+ENSDARG00000102470 7 0.825035359668146 13.4793918534294 16.3379565438882 1.10737149331994e-09 2.25054799825723e-06
+ENSDARG00000104836 7 1.0201341649907 17.1513950198419 16.8128816860067 1.79596375972667e-09 2.73749776076337e-06
+ENSDARG00000104197 7 0.868813330133413 13.2077072533743 15.2020080669644 2.27590161725937e-09 2.77523443208607e-06
+ENSDARG00000102167 7 0.911623267267556 12.5281341487954 13.7426660755889 6.03157787269791e-09 6.12908838163986e-06
+ENSDARG00000105195 7 1.35837446108669 20.6382812121625 15.193366632977 1.20671859497662e-08 1.05105189622463e-05
+ENSDARG00000105669 7 1.55320812115904 19.4772872937536 12.5400369908053 8.3653757257818e-08 6.37546197501146e-05
+ENSDARG00000102820 7 1.12752840077096 11.8419301998565 10.5025560258699 1.31966552783421e-07 8.94000080356132e-05
+ENSDARG00000092989 7 0.133042434280628 1.21637077531351 9.14272789648302 2.82608004083509e-07 0.000172306100089716
+ENSDARG00000061806 7 0.13278988077121 1.12194957012091 8.44905924762421 7.25529240779189e-07 0.000402141071002793
+ENSDARG00000095512 7 0.134733887854507 1.08703031970933 8.06798005326739 1.27119959332606e-06 0.000645875326709081
+ENSDARG00000090634 7 0.14895440642195 1.13152352961684 7.5964421382173 1.67131715307221e-06 0.000689864250270158
+ENSDARG00000087555 7 0.106854974051793 0.876076138239269 8.19873989033614 1.8103703467808e-06 0.000689864250270158
+ENSDARG00000069269 7 0.131991994835001 1.03283452343888 7.82497851274993 2.01967640768832e-06 0.000724351003392688
+ENSDARG00000059558 7 0.112699471961133 0.967793901919788 8.58738630340302 3.00038333622434e-06 0.000888688802910736
+ENSDARG00000060566 7 0.127846770606366 1.01035836252462 7.90288528785342 3.78083155119976e-06 0.000992894397782283
+ENSDARG00000100206 7 0.139832328948304 1.04998427596811 7.5088806992286 4.54325865418129e-06 0.000992894397782283
+ENSDARG00000057206 7 0.121885624201679 0.88338782626096 7.24767856789453 4.55979057534917e-06 0.000992894397782283
+ENSDARG00000070623 7 0.12670584582223 0.943766658477006 7.44848552450473 5.87432370429556e-06 0.00110819712277626
+ENSDARG00000100514 7 0.121454028840368 0.820406006163069 6.75486860334098 7.45177975757828e-06 0.00116897636495374
+ENSDARG00000039265 7 0.131635113592875 0.87126351316452 6.6187773868543 9.18440046329954e-06 0.00133326880058898
+ENSDARG00000095904 7 0.168129332968718 1.08581712830248 6.45822539785194 1.03525068635208e-05 0.00139894259529663
+ENSDARG00000039350 7 0.133011711683714 0.897490439418404 6.74745425088979 1.06942592337219e-05 0.00139894259529663
+ENSDARG00000070512 7 0.12670239660567 0.910072943888678 7.18276029711621 1.10515908767776e-05 0.00139894259529663
+ENSDARG00000103551 8 1.61835767565622 32.2654393890171 19.93714978732 1.97522608849965e-06 0.0120429534615824
+ENSDARG00000078383 8 0.182610070366458 2.60621132144157 14.2720021749703 1.6366673021414e-05 0.0447464228757837
+ENSDARG00000093799 8 0.115321017732354 1.62941087246693 14.1293487042283 2.20172656433248e-05 0.0447464228757837
+ENSDARG00000036625 8 0.119337255991682 1.48171990557204 12.4162391137543 8.39663841121717e-05 0.127985760982978
+ENSDARG00000016706 8 0.180025642511508 1.82486224560436 10.1366795315712 0.000126325160000158 0.154040900104192
+ENSDARG00000040251 8 0.121540951107174 1.29918699186992 10.6892942669529 0.000198034398721646 0.201235954834313
+ENSDARG00000098674 8 0.253812764860557 2.21906493621457 8.74292093793513 0.000293366486612692 0.255522209839655
+ENSDARG00000098856 8 0.194513509828675 1.64663383642527 8.46539573459756 0.000451769293400039 0.296721325111977
+ENSDARG00000062226 8 0.144813536626749 1.38335068305012 9.55263378875725 0.000474939776632199 0.296721325111977
+ENSDARG00000075123 8 0.142439266402834 1.40532056857682 9.86610366696508 0.00048666774661633 0.296721325111977
+ENSDARG00000070239 8 0.154515334275144 1.27289156626506 8.23796273836765 0.000570475520527726 0.316199022605232
+ENSDARG00000026180 8 0.151758427938041 1.41564289946672 9.32826544595394 0.000683459166751383 0.347254211640265
+ENSDARG00000104786 8 0.182483274181232 1.61787042996763 8.8658559927024 0.00078762411588287 0.369395710349066
+ENSDARG00000101061 8 0.255483815147335 1.62613690189592 6.36493118344166 0.00150635451453941 0.61883047685698
+ENSDARG00000016584 8 0.135272462199637 0.880366460381022 6.50809814551733 0.00158197684628705 0.61883047685698
+ENSDARG00000070256 8 0.203213690445973 1.26976802854965 6.24843742448165 0.00178015471505539 0.61883047685698
+ENSDARG00000062745 8 0.130428963634169 0.955091918456498 7.32269805604966 0.00182445112094621 0.61883047685698
+ENSDARG00000086037 8 0.19632007891506 1.29918699186992 6.61769799120764 0.00182695564760138 0.61883047685698
+ENSDARG00000027310 8 0.193675103177481 1.44901164174846 7.48166190685131 0.00211840042255122 0.678671506770642
+ENSDARG00000103109 8 0.14293938597264 0.936026560054929 6.54841598545899 0.00240745117064372 0.678671506770642
+ENSDARG00000078352 8 0.177346649454539 1.15788746142844 6.52895030715114 0.0024876207141355 0.678671506770642
+ENSDARG00000035389 8 0.143574445102194 1.00421593036345 6.99439186164828 0.0026995869399452 0.678671506770642
+ENSDARG00000103106 8 0.175526172559138 1.23041862190788 7.00988692437495 0.0027017171947583 0.678671506770642
+ENSDARG00000007257 8 0.157933075856061 0.866671316548008 5.48758587680447 0.0028384639169755 0.678671506770642
+ENSDARG00000010596 8 0.110516369140454 0.836156159426777 7.56590327686312 0.00297745919336174 0.678671506770642
diff -r 000000000000 -r ff7cd3c7c1df test-data/matrix.pdf
Binary file test-data/matrix.pdf has changed
diff -r 000000000000 -r ff7cd3c7c1df test-data/matrix.rdat
Binary file test-data/matrix.rdat has changed
diff -r 000000000000 -r ff7cd3c7c1df test-data/matrix.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/matrix.tabular Thu Nov 22 04:43:00 2018 -0500
@@ -0,0 +1,6170 @@
+ P1_B1_ACATGG P1_B1_AGTAGG P1_B1_ATACGG P1_B1_ATCCAC P1_B1_ATCTCC P1_B1_CAATGC P1_B1_CAGGAA P1_B1_CCAGTA P1_B1_CCTATG P1_B1_GCAATG P1_B1_GCGTTA P1_B1_GGAATC P1_B1_GGATCA P1_B1_GGTGTA P1_B1_GTAACC P1_B1_GTATCG P1_B1_TATCGC P1_B1_TGATCG P1_B1_TTACGC P1_B1_TTGCAC P1_B1_TTGGCA P1_B2_ACGTAC P1_B2_ACTCGA P1_B2_ACTTCG P1_B2_AGGATC P1_B2_AGTGCA P1_B2_ATCACG P1_B2_CAGAAG P1_B2_CATGCA P1_B2_CATGTC P1_B2_CCATAG P1_B2_CTAAGC P1_B2_CTGTTG P1_B2_GCAACA P1_B2_GTCTCA P1_B2_GTGAAG P1_B2_GTGATC P1_B2_TCTTGC P1_B2_TGCAGA P1_B2_TGGTGA P1_B2_TTCACC P2_B3_AAGCAC P2_B3_AAGTGC P2_B3_ACATGG P2_B3_ACGGTA P2_B3_AGATGC P2_B3_AGTAGG P2_B3_ATACGG P2_B3_ATCTCC P2_B3_ATGGAC P2_B3_CAGGAA P2_B3_CCAGTA P2_B3_CCTATG P2_B3_CGCATA P2_B3_GCAATG P2_B3_GCAGAA P2_B3_GCGTTA P2_B3_GGAATC P2_B3_GGATCA P2_B3_GGTGTA P2_B3_GTAACC P2_B3_GTATCG P2_B3_TACCAC P2_B3_TACGCA P2_B3_TGATCG P2_B3_TTACGC P2_B3_TTGCAC P2_B4_AACGAG P2_B4_AAGCCA P2_B4_ACAAGC P2_B4_ACGTAC P2_B4_ACTCGA P2_B4_ACTTCG P2_B4_AGCTAG P2_B4_AGCTTC P2_B4_AGGATC P2_B4_AGTGCA P2_B4_ATCACG P2_B4_ATGTCG P2_B4_CACCAA P2_B4_CAGGAA P2_B4_CATGTC P2_B4_CCATAG P2_B4_CTAAGC P2_B4_CTGTTG P2_B4_GAGTGA P2_B4_GATCGA P2_B4_GATCTG P2_B4_GCAACA P2_B4_GTCTCA P2_B4_GTGAAG P2_B4_GTGATC P2_B4_GTGGAA P2_B4_TAACGG P2_B4_TCTTGC P2_B4_TGAGGA P2_B4_TGGTGA P2_B4_TGGTTG P2_B4_TGTACG P2_B4_TGTCGA P2_B4_TTCACC
+ENSDARG00000000018 0 0 0 0 2 0 1 0 1 0 1 0 0 0 4 1 2 1 0 0 1 1 2 0 0 1 3 3 1 0 2 0 0 0 0 0 2 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ENSDARG00000000019 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 3 1 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 1 3 0 0 0 0
+ENSDARG00000000069 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 3 1 0 1 1 0 0 0 1 0 0 0 0 0 0 0 2 0 0 0 0
+ENSDARG00000000086 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 3 0 1 0 0 1 0 1 0 0 0 0 1 1 1 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ENSDARG00000000161 1 0 2 0 0 0 0 0 1 0 1 0 0 1 2 0 1 1 0 0 1 0 1 1 0 1 2 2 0 2 0 0 0 1 2 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ENSDARG00000000183 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 1 1 0 1 1 0 0 0 0 0 0 0 1 0 1 0 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ENSDARG00000000189 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 2 0 0 1 0 1 0 1 0 1 0 1 0 0 0 0 0 0 1 0 1 0 1 0 0 0 0 0 0 0 0 3 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 1
+ENSDARG00000000229 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1 1 1 1 1 0 0 1 1 1 2 0 1 1 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 1 1 0 1 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 1
+ENSDARG00000000241 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 6 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ENSDARG00000000370 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 5 0 0 0 2 0 0 2 1 0 2 1 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 3 2 0 1 0 0 2 0 0 0 0
+ENSDARG00000000394 0 0 0 1 0 0 0 0 2 0 1 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 1 1 0 1 0 0 0 0 0 1 2 0 0 0 0 0 0 0 0 1 0 0 0 2 0 1 2 0 1 1 1 0 0 0 0 0 0 2 0 0 0 0 1 2 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0
+ENSDARG00000000442 0 0 1 0 0 0 0 1 0 2 0 1 1 0 0 0 0 2 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ENSDARG00000000489 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 6 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ENSDARG00000000551 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 2 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ENSDARG00000000568 0 0 0 0 2 0 2 0 0 0 0 4 0 0 0 0 2 2 1 3 3 0 1 0 0 0 0 0 0 0 0 0 0 2 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 1 0 0 1 1 0 0 0 0 2 0 0 1 0 0 0 0 3 0 1
+ENSDARG00000000606 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 5 0 1 0 0 0 0 1 3 0 0 0 1 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ENSDARG00000000631 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 1 1 1 0 2 1 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ENSDARG00000000666 0 0 1 0 0 1 0 0 1 1 2 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 2 0 0 0 1 0 0 3 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ENSDARG00000000767 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 1 0 1 3 0 0 0 1 0 0 0 1 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 2 2 1
+ENSDARG00000000779 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 3 0 0 0 0 2 0 0 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 1 1 0 1 0 0 0 0 2 0 1 0 0 0 1 1 2 0 0 0 1 0 1 0 0 1 1
+ENSDARG00000000796 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 1 0 0 1 0 1 3 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 2 1 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 1 1 0 1 0 0
+ENSDARG00000000853 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 2 0 0 0 1 5 1 0 0 0 0 0 1 1 1 0 0 0 0 0 1 0 1 1 0 0 1 0 2 0 0 1 0 1 0 1 0 1 2 0 0 2 0 0 2 0 0 0 0 0 0 0 1 0 2 0
+ENSDARG00000000857 1 1 0 0 1 0 1 0 1 0 0 1 0 0 0 0 1 1 0 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1 2 1 0 2 0 0 1 0 1 0 0 0 0 0 1 0 0 0 0 1 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
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+ENSDARG00000108961 0 1 0 1 0 1 0 0 3 3 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ENSDARG00000109030 39 2 32 45 43 1 21 3 28 3 94 60 0 26 90 0 37 88 122 6 69 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ENSDARG00000109181 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 2 0 1 2 2 1 0 2 1 2 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
diff -r 000000000000 -r ff7cd3c7c1df test-data/matrix2.genelist
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/matrix2.genelist Thu Nov 22 04:43:00 2018 -0500
@@ -0,0 +1,201 @@
+n mean.ncl mean.cl fc pv padj
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+ENSDARG00000109030 1 0.186711263967539 34.6842724288799 185.764220603798 2.48233981248329e-19 7.56741291835532e-16
+ENSDARG00000108379 1 0.168199368419563 24.3874482842581 144.991319012715 4.11994031997326e-19 8.37309204362565e-16
+ENSDARG00000107599 1 0.194980763882093 20.9729826342942 107.564367975175 3.56470297051077e-18 5.43349850280104e-15
+ENSDARG00000107321 1 0.1 1.94683879586459 19.4683879586459 1.39905888784068e-09 1.70601240783292e-06
+ENSDARG00000105564 1 0.1 1.72137476189456 17.2137476189456 5.11677986670882e-09 5.19950114122061e-06
+ENSDARG00000090447 1 0.1 1.4302236712519 14.302236712519 3.51620742912878e-08 3.06261667077116e-05
+ENSDARG00000079591 1 0.11578454541401 1.47825950354764 12.767330028907 4.83701028926633e-08 3.6864064667071e-05
+ENSDARG00000107138 1 0.118643244515052 1.63372529702772 13.7700659123533 8.59237265783686e-08 5.36793599520202e-05
+ENSDARG00000041060 1 0.11578454541401 1.4382199783801 12.421519411226 8.84781911763433e-08 5.36793599520202e-05
+ENSDARG00000077004 1 0.1 1.29299827494356 12.9299827494356 1.0364347799037e-07 5.36793599520202e-05
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out_traject_inspect_allthree.tabular Thu Nov 22 04:43:00 2018 -0500
@@ -0,0 +1,15 @@
+"x"
+"Me2" 3.1519849710225
+"Ddx21" 2.66820084388138
+"Rnf128" 2.66057393206263
+"Vamp8" 2.59546068208913
+"Esrp1" 2.49514855152429
+"Mff" 2.40847120142661
+"Sugt1" 2.40135465960895
+"Smoc2" 2.33534839241479
+"Nap1l1" 2.30643227361057
+"Tbcb" 2.30035172881174
+"Nisch" 2.29988099912322
+"Adipor1" 2.2844835138172
+"Ppa2" 2.27481682067412
+"Taf9" 2.22301148117027
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diff -r 000000000000 -r ff7cd3c7c1df test-data/out_traject_inspect_stemid.pdf
Binary file test-data/out_traject_inspect_stemid.pdf has changed
diff -r 000000000000 -r ff7cd3c7c1df test-data/out_traject_inspect_stemid.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out_traject_inspect_stemid.tabular Thu Nov 22 04:43:00 2018 -0500
@@ -0,0 +1,11 @@
+"x"
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+"Cox4i1" 2.40532524867387
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+"Ap1s1" 2.29422010626431
+"Tor1aip2" 2.27751793076177
+"Hsd17b12" 2.22740668789088
+"Rangap1" 2.21481286601604
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diff -r 000000000000 -r ff7cd3c7c1df test-data/use.intestinal
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/use.intestinal Thu Nov 22 04:43:00 2018 -0500
@@ -0,0 +1,2 @@
+test
+test 0