[CHNOSZ-commits] r119 - in pkg/CHNOSZ: . R demo inst inst/extdata/abundance inst/extdata/protein man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sun Jan 1 11:48:02 CET 2017
Author: jedick
Date: 2017-01-01 11:48:01 +0100 (Sun, 01 Jan 2017)
New Revision: 119
Added:
pkg/CHNOSZ/demo/bugstab.R
pkg/CHNOSZ/inst/extdata/abundance/microbes.csv
pkg/CHNOSZ/inst/extdata/protein/microbial.aa.csv
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/R/examples.R
pkg/CHNOSZ/demo/00Index
pkg/CHNOSZ/inst/NEWS
pkg/CHNOSZ/man/examples.Rd
pkg/CHNOSZ/man/extdata.Rd
Log:
add demo bugstab.R
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2016-12-21 11:10:04 UTC (rev 118)
+++ pkg/CHNOSZ/DESCRIPTION 2017-01-01 10:48:01 UTC (rev 119)
@@ -1,6 +1,6 @@
-Date: 2016-12-21
+Date: 2017-01-01
Package: CHNOSZ
-Version: 1.0.8-6
+Version: 1.0.8-7
Title: Chemical Thermodynamics and Activity Diagrams
Author: Jeffrey Dick
Maintainer: Jeffrey Dick <j3ffdick at gmail.com>
Modified: pkg/CHNOSZ/R/examples.R
===================================================================
--- pkg/CHNOSZ/R/examples.R 2016-12-21 11:10:04 UTC (rev 118)
+++ pkg/CHNOSZ/R/examples.R 2017-01-01 10:48:01 UTC (rev 119)
@@ -32,7 +32,7 @@
demos <- function(which=c("sources", "NaCl", "density",
"nucleobase", "ORP", "revisit", "findit",
"ionize", "buffer", "yeastgfp", "mosaic",
- "copper", "solubility", "wjd", "dehydration"), to.file=FALSE) {
+ "copper", "solubility", "wjd", "dehydration", "bugstab"), to.file=FALSE) {
# run one or more demos from CHNOSZ with ask=FALSE, and return the value of the last one
for(i in 1:length(which)) {
# say something so the user sees where we are
@@ -41,7 +41,10 @@
msgout("demos: skipping dehydration demo as to.file is FALSE\n")
next
} else msgout(paste("demos: running '", which[i], "'\n", sep=""))
- if(to.file & !which[i]=="dehydration") png(paste(which[i],"%d.png",sep=""),width=500,height=500,pointsize=12)
+ if(to.file & !which[i]=="dehydration") {
+ if(which[i]=="bugstab") png(paste(which[i], "%d.png", sep=""), width=700, height=500, pointsize=12)
+ else png(paste(which[i], "%d.png", sep=""), width=500, height=500, pointsize=12)
+ }
out <- demo(which[i], package="CHNOSZ", character.only=TRUE, echo=FALSE, ask=FALSE)
if(to.file & !which[i]=="dehydration") dev.off()
}
Modified: pkg/CHNOSZ/demo/00Index
===================================================================
--- pkg/CHNOSZ/demo/00Index 2016-12-21 11:10:04 UTC (rev 118)
+++ pkg/CHNOSZ/demo/00Index 2017-01-01 10:48:01 UTC (rev 119)
@@ -13,3 +13,4 @@
solubility solubility of calcite or CO2(gas) as a function of pH
wjd run.wjd() with proteins: cell periphery of yeast
dehydration log K of dehydration reactions; SVG file contains tooltips and links
+bugstab formation potential of microbial proteins in colorectal cancer
Added: pkg/CHNOSZ/demo/bugstab.R
===================================================================
--- pkg/CHNOSZ/demo/bugstab.R (rev 0)
+++ pkg/CHNOSZ/demo/bugstab.R 2017-01-01 10:48:01 UTC (rev 119)
@@ -0,0 +1,67 @@
+# formation potential of microbial proteins in colorectal cancer
+# based on "bugstab" function in Supporting Information of Dick, 2016
+# (http://dx.doi.org/10.7717/peerj.2238)
+
+# resolution for plots
+res <- 500
+# basis can be "AA" or "CHNOS"
+basis <- "AA"
+layout(cbind(matrix(sapply(list(c(1, 2), c(3, 4)), function(x) rep(rep(x, each=3), 3)), nrow=6, byrow=TRUE),
+ matrix(rep(c(0, 5, 5, 5, 5, 0), each=4), nrow=6, byrow=TRUE)))
+par(mar=c(3.3, 3.3, 1.5, 1.5), mgp=c(2.1, 0.7, 0), xaxs="i", yaxs="i", las=1, cex=0.9)
+# read bioproject ids, species names
+mfile <- system.file("extdata/abundance/microbes.csv", package="CHNOSZ")
+bugs <- read.csv(mfile, as.is=TRUE)
+# where to keep the locations of healthy zones
+healthbugs <- list()
+if(basis=="CHNOS") {
+ O2 <- c(-85, -65, res)
+ H2O <- c(-15, 5, res)
+} else {
+ O2 <- c(-75, -55, res)
+ H2O <- c(-10, 10, res)
+}
+# the datasets that are considered
+datasets <- c("WCQ+12", "ZTV+14", "CTB+14", "FLJ+15")
+# colors
+blue <- "#4A6FE3"
+lightblue <- "#9DA8E2"
+neutral <- "#E2E2E2"
+lightred <- "#E495A5"
+red <- "#D33F6A"
+# labels
+logfO2lab <- expression(log*italic("f")[O[2]*group("(", italic("g"), ")")])
+logaH2Olab <- expression(log*italic("a")[H[2]*O*group("(", italic("liq"), ")")])
+for(i in 1:4) {
+ ibug <- bugs$study==datasets[i] & (is.na(bugs$logodds) | abs(bugs$logodds) > 0.15)
+ # get amino acid compositions
+ aafile <- system.file("extdata/protein/microbial.aa.csv", package="CHNOSZ")
+ microbial.aa <- read.csv(aafile, stringsAsFactors=FALSE)
+ aa <- microbial.aa[match(bugs$bioproject[ibug], microbial.aa$organism), ]
+ ip <- add.protein(aa)
+ # set up system, calculate relative stabilities
+ col <- ifelse(bugs$upcan[ibug], lightred, lightblue)
+ basis(basis)
+ a <- affinity(O2=O2, H2O=H2O, iprotein=ip, T=37)
+ names <- bugs$abbrv[ibug]
+ d <- CHNOSZ::diagram(a, names=names, fill=col, as.residue=TRUE, tplot=FALSE, xlab=logfO2lab, ylab=logaH2Olab)
+ if(i==1) title(main="fecal 16S rRNA", cex.main=1)
+ if(i==2) title(main="fecal metagenome (ZTV+14)", cex.main=1)
+ if(i==3) title(main="co-abundance groups", cex.main=1)
+ if(i==4) title(main="fecal metagenome (FLJ+15)", cex.main=1)
+ box()
+ label.figure(LETTERS[i], yfrac=0.96, paren=FALSE, font=2, cex=1)
+ # store locations of healthy bug zones
+ p <- d$predominant
+ p[p %in% which(bugs$upcan[ibug])] <- 0
+ p[p != 0] <- 1
+ healthbugs[[i]] <- p
+}
+# now show the healthy zones
+xs <- seq(O2[1], O2[2], length.out=O2[3])
+ys <- seq(H2O[1], H2O[2], length.out=H2O[3])
+hhh <- healthbugs[[1]] + healthbugs[[2]] + healthbugs[[3]] + healthbugs[[4]]
+image(xs, ys, hhh, col=c(red, lightred, neutral, lightblue, blue), useRaster=TRUE, xlab=logfO2lab, ylab=logaH2Olab)
+title(main="cumulative stability count")
+box()
+label.figure("E", yfrac=0.96, paren=FALSE, font=2, cex=1)
Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS 2016-12-21 11:10:04 UTC (rev 118)
+++ pkg/CHNOSZ/inst/NEWS 2017-01-01 10:48:01 UTC (rev 119)
@@ -1,4 +1,4 @@
-CHANGES IN CHNOSZ 1.0.8-6 (2016-12-21)
+CHANGES IN CHNOSZ 1.0.8-7 (2017-01-01)
--------------------------------------
- Add "AA" as a keyword for preset species in basis() (cysteine,
@@ -22,6 +22,8 @@
(citric acid cycle metabolites; thioester species have been kept) and
from Dick et al., 2006 (methionine and [Met]).
+- Add demo bugstab.R.
+
CHANGES IN CHNOSZ 1.0.8 (2016-05-28)
------------------------------------
Added: pkg/CHNOSZ/inst/extdata/abundance/microbes.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/abundance/microbes.csv (rev 0)
+++ pkg/CHNOSZ/inst/extdata/abundance/microbes.csv 2017-01-01 10:48:01 UTC (rev 119)
@@ -0,0 +1,75 @@
+species,abbrv,bioproject,study,upcan,abundance,logodds,dx,dy,ZC,nH2O
+"B. vulgatus",Bvu,PRJNA13378,WCQ+12,FALSE,21.49,NA,-0.01,-0.005,-0.1625,-0.8003
+"B. uniformis",Bun,PRJNA18195,WCQ+12,FALSE,21.49,NA,0.007,0,-0.1622,-0.7996
+"R. intestinalis",Rin,PRJNA30005,WCQ+12,FALSE,3.59,NA,-0.01,-0.005,-0.1637,-0.7583
+"A. indistinctus",Ain,PRJNA46373,WCQ+12,FALSE,1.11,NA,0.002,0,-0.1545,-0.7725
+"E. rectale",Ere,PRJNA29071,WCQ+12,FALSE,0.52,NA,-0.007,0,-0.1676,-0.75
+"P. excrementihominis",Pex,PRJNA48497,WCQ+12,FALSE,0.44,NA,0,0,-0.1743,-0.7269
+"P. gingivalis",Pgi,PRJNA48,WCQ+12,TRUE,1.74,NA,-0.01,-0.005,-0.1613,-0.7683
+"E. coli",Eco,PRJNA47121,WCQ+12,TRUE,2.45,NA,0,0,-0.1588,-0.7491
+"E. faecalis",Efa,PRJNA57669,WCQ+12,TRUE,2.4,NA,-0.01,-0.005,-0.1887,-0.7337
+"S. infantarius",Sin,PRJNA20527,WCQ+12,TRUE,1.19,NA,-0.002,0,-0.1854,-0.7303
+"P. stomatis",Pst,PRJNA34073,WCQ+12,TRUE,0.59,NA,0,0,-0.1914,-0.7052
+"B. fragilis",Bfr,PRJNA58195,WCQ+12,TRUE,NA,NA,0,0,-0.1685,-0.7903
+"B. longum",Blo,PRJNA57939,CTB+14,FALSE,NA,NA,0,0,-0.1226,-0.7404
+"F. prausnitzii",Fpr,PRJNA39151,CTB+14,FALSE,NA,NA,0,0,-0.1535,-0.7434
+"F. nucleatum",Fnu,PRJNA49043,CTB+14,TRUE,NA,NA,0,0,-0.2242,-0.7062
+"P. copri",Pco,PRJNA30025,CTB+14,TRUE,NA,NA,0,0,-0.1619,-0.7884
+Coprobacillus,Csp,PRJNA32495,CTB+14,TRUE,NA,NA,0,0,-0.1958,-0.7464
+"F. nucleatum subsp. vincentii",Fnv,PRJNA1419,ZTV+14,TRUE,NA,1.39,0,-0.01,-0.2202,-0.7123
+"F. nucleatum subsp. animalis",Fna,PRJNA32501,ZTV+14,TRUE,NA,0.66,0,0,-0.2232,-0.7083
+"P. stomatis",Pst,PRJNA34073,ZTV+14,TRUE,NA,0.56,-0.004,0,-0.1914,-0.7052
+"P. asaccharolytica",Pas,PRJNA51745,ZTV+14,TRUE,NA,0.38,0,-0.01,-0.1559,-0.7547
+"C. symbiosum",Csy,PRJNA18183,ZTV+14,TRUE,NA,0.34,0.01,-0.006,-0.1719,-0.7393
+"C. hylemonae",Chy,PRJNA30369,ZTV+14,TRUE,NA,0.18,0,0,-0.1676,-0.7341
+"L. salivarius",Lsa,PRJNA31503,ZTV+14,TRUE,NA,0.16,0,0,-0.1896,-0.7298
+"C. scindens",Csc,PRJNA18175,ZTV+14,FALSE,NA,-0.16,0.008,-0.01,-0.1713,-0.741
+"E. eligens",Eel,PRJNA29073,ZTV+14,FALSE,NA,-0.16,-0.008,-0.002,-0.1725,-0.7363
+"M. stadtmanae",Mst,PRJNA15579,ZTV+14,FALSE,NA,-0.18,0,0,-0.1832,-0.7028
+"P. succinatutens",Psu,PRJNA48505,ZTV+14,FALSE,NA,-0.23,0,0,-0.1811,-0.7188
+Ruminococcus,Rsp,PRJNA18179,ZTV+14,FALSE,NA,-0.3,0,-0.01,-0.1733,-0.7467
+"S. salivarius",Ssa,PRJNA34091,ZTV+14,FALSE,NA,-0.54,-0.01,-0.005,-0.1751,-0.74
+"Acidaminococcus intestini DSM 21505",Ain,PRJNA188796,FLJ+15,TRUE,NA,NA,NA,NA,-0.1749,-0.7285
+"Alistipes finegoldii DSM 17242",Afi,PRJNA40775,FLJ+15,TRUE,NA,NA,NA,NA,-0.1427,-0.7847
+"Alistipes onderdonkii WAL 8169 = DSM 19147",Aon,PRJNA174975,FLJ+15,TRUE,NA,NA,NA,NA,-0.1398,-0.7934
+"Alistipes putredinis DSM 17216",Apu,PRJNA19655,FLJ+15,TRUE,NA,NA,NA,NA,-0.1533,-0.7724
+"Bacteroides caccae MR1_13",Bca,PRJNA212635,FLJ+15,TRUE,NA,NA,NA,NA,-0.1683,-0.7914
+"Bacteroides dorei DSM 17855",Bdo,PRJNA27831,FLJ+15,TRUE,NA,NA,-0.01,-0.005,-0.1633,-0.8005
+"Bacteroides eggerthii DSM 20697",Beg,PRJNA27827,FLJ+15,TRUE,NA,NA,NA,NA,-0.1647,-0.7924
+"Bacteroides massiliensis B84634 = Timone 84634 = DSM 17679 = JCM 13223",Bma,PRJNA169707,FLJ+15,TRUE,NA,NA,NA,NA,-0.1657,-0.7873
+"Bacteroides ovatus strain:KLE1656",Bov,PRJNA257718,FLJ+15,TRUE,NA,NA,0.01,-0.005,-0.1613,-0.8002
+"Bacteroides sp. 1_1_30",B30,PRJNA41955,FLJ+15,TRUE,NA,NA,NA,NA,-0.1614,-0.7975
+"Bacteroides sp. 4_1_36",B36,PRJNA39357,FLJ+15,TRUE,NA,NA,NA,NA,-0.1606,-0.7975
+"Bacteroides vulgatus ATCC 8482",Bvu,PRJNA13378,FLJ+15,TRUE,NA,NA,NA,NA,-0.1625,-0.8003
+"Bacteroides xylanisolvens XB1A",Bxy,PRJNA197168,FLJ+15,TRUE,NA,NA,NA,NA,-0.1625,-0.7973
+"Bilophila wadsworthia ATCC 49260",Bwa,PRJNA223063,FLJ+15,TRUE,NA,NA,NA,NA,-0.1586,-0.7368
+"Burkholderiales bacterium 1_1_47",Bba,PRJNA41965,FLJ+15,TRUE,NA,NA,NA,NA,-0.1738,-0.728
+"butyrate-producing bacterium SS3/4",But,PRJNA197159,FLJ+15,TRUE,NA,NA,0,0,-0.1656,-0.7385
+"Clostridium asparagiforme DSM 15981",Cas,PRJNA29263,FLJ+15,TRUE,NA,NA,0,-0.01,-0.1562,-0.7537
+"Clostridium bolteae WAL-14578",Cbo,PRJNA46383,FLJ+15,TRUE,NA,NA,NA,NA,-0.1599,-0.7509
+"Clostridium hathewayi DSM 13479",Cha,PRJNA30755,FLJ+15,TRUE,NA,NA,NA,NA,-0.1643,-0.7658
+"Clostridium symbiosum ATCC 14940",Csy,PRJNA18183,FLJ+15,TRUE,NA,NA,NA,NA,-0.1719,-0.7393
+"Dialister invisus DSM 15470",Din,PRJNA33143,FLJ+15,TRUE,NA,NA,NA,NA,-0.1727,-0.7398
+"Escherichia coli NC101",Eco,PRJNA47121,FLJ+15,TRUE,NA,NA,NA,NA,-0.1588,-0.7491
+"Fusobacterium sp. oral taxon 370 str. F0437",Fsp,PRJNA50399,FLJ+15,TRUE,NA,NA,0,0,-0.2211,-0.7127
+"Gemella morbillorum CC57F",Gmo,PRJNA71551,FLJ+15,TRUE,NA,NA,NA,NA,-0.2132,-0.7123
+"Lachnospiraceae bacterium 3_1_46FAA",L46,PRJNA40027,FLJ+15,TRUE,NA,NA,NA,NA,-0.1665,-0.7388
+"Lachnospiraceae bacterium 3_1_57FAA_CT1",L57,PRJNA39383,FLJ+15,TRUE,NA,NA,0,0,-0.166,-0.7807
+"Lachnospiraceae bacterium 7_1_58FAA",L58,PRJNA39397,FLJ+15,TRUE,NA,NA,NA,NA,-0.1416,-0.7557
+"Odoribacter splanchnicus DSM 20712",Osp,PRJNA43469,FLJ+15,TRUE,NA,NA,NA,NA,-0.1719,-0.7892
+"Parabacteroides distasonis ATCC 8503",Pdi,PRJNA13485,FLJ+15,TRUE,NA,NA,NA,NA,-0.1693,-0.7889
+"Parabacteroides merdae ATCC 43184",Pme,PRJNA18193,FLJ+15,TRUE,NA,NA,NA,NA,-0.1683,-0.7898
+"Paraprevotella clara YIT 11840",Pcl,PRJNA48501,FLJ+15,TRUE,NA,NA,0,-0.012,-0.1474,-0.8098
+"Parvimonas micra ATCC 33270",Pmi,PRJNA18169,FLJ+15,TRUE,NA,NA,NA,NA,-0.2178,-0.7185
+"Peptostreptococcus stomatis DSM 17678",Pst,PRJNA34073,FLJ+15,TRUE,NA,NA,0,0,-0.1914,-0.7052
+"Porphyromonas somerae DSM 23386",Pso,PRJNA165425,FLJ+15,TRUE,NA,NA,NA,NA,-0.1652,-0.7671
+"Prevotella copri DSM 18205",Pco,PRJNA30025,FLJ+15,TRUE,NA,NA,NA,NA,-0.1619,-0.7884
+"Ruminococcaceae bacterium D16",Rba,PRJNA42541,FLJ+15,TRUE,NA,NA,0.01,-0.005,-0.1557,-0.7426
+"Sutterella wadsworthensis HGA0223",Swa,PRJNA169488,FLJ+15,TRUE,NA,NA,NA,NA,-0.1575,-0.7254
+"Veillonella atypica UC1_FAA_A",Vat,PRJNA212673,FLJ+15,TRUE,NA,NA,NA,NA,-0.1724,-0.7348
+"Actinomyces viscosus C505",Avi,PRJNA38743,FLJ+15,FALSE,NA,NA,0,0,-0.1168,-0.6981
+"Bifidobacterium animalis subsp. lactis AD011",Ban,PRJNA19423,FLJ+15,FALSE,NA,NA,0,0,-0.118,-0.7549
+"Clostridium sp. SS2/1",Csp,PRJNA18201,FLJ+15,FALSE,NA,NA,0.002,-0.012,-0.1861,-0.7338
+"Ruminococcus sp. 5_1_39BFAA",Rsp,PRJNA32503,FLJ+15,FALSE,NA,NA,0,0,-0.1675,-0.7499
+"Streptococcus mutans",Smu,PRJNA13225,FLJ+15,FALSE,NA,NA,-0.004,0,-0.1934,-0.7359
+"Streptococcus thermophilus",Sth,PRJNA13799,FLJ+15,FALSE,NA,NA,0,0,-0.1854,-0.732
Added: pkg/CHNOSZ/inst/extdata/protein/microbial.aa.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/protein/microbial.aa.csv (rev 0)
+++ pkg/CHNOSZ/inst/extdata/protein/microbial.aa.csv 2017-01-01 10:48:01 UTC (rev 119)
@@ -0,0 +1,69 @@
+protein,organism,ref,abbrv,chains,Ala,Cys,Asp,Glu,Phe,Gly,His,Ile,Lys,Leu,Met,Asn,Pro,Gln,Arg,Ser,Thr,Val,Trp,Tyr
+mean,PRJNA13225,NA,NA,1,22.0408163265306,1.68673469387755,16.7071428571429,18.8836734693878,14.0489795918367,18.5051020408163,5.78112244897959,22.8658163265306,21.9331632653061,29.9397959183673,7.16428571428572,14.3311224489796,9.32448979591837,12.0540816326531,11.5459183673469,18.5683673469388,16.5933673469388,19.4790816326531,2.57704081632653,11.3882653061225
+mean,PRJNA13378,NA,NA,1,25.6036900369003,4.84969249692498,20.3945879458796,24.7416974169742,17.0792127921279,25.5567035670357,7.4029520295203,25.7269372693727,25.4361623616236,33.7136531365314,10.5645756457565,19.5377613776139,13.9052890528905,12.7448954489544,17.5675276752767,22.4142681426814,20.7950799507996,23.5758917589175,5.00123001230015,16.9778597785979
+mean,PRJNA13485,NA,NA,1,26.0537662337662,4.43012987012987,20.8332467532467,24.4075324675324,17.518961038961,25.718961038961,6.78051948051948,26.1615584415584,24.1888311688311,35.0501298701298,10.2651948051948,18.6194805194805,14.6511688311688,12.3592207792208,17.9098701298701,23.6522077922078,20.6431168831169,24.4311688311688,4.65142857142856,16.6955844155844
+mean,PRJNA13799,NA,NA,1,20.9127031908489,1.53100541842264,16.3756773028296,19.151715833835,12.8121613485852,18.4455147501505,5.30042143287177,20.6387718242023,19.1896447922938,27.6616496086695,7,12.7814569536424,9.12703190848886,10.524984948826,11.4954846478025,17.3257074051776,15.8609271523179,19.9554485249849,2.32510535821794,10.4274533413606
+mean,PRJNA1419,NA,NA,1,14.272,2.13066666666667,14.608,21.2093333333334,12.9333333333333,16.7755555555556,3.18933333333334,26.4719999999999,27.2102222222223,24.5857777777777,6.37333333333333,17.2204444444444,6.82933333333332,5.88399999999999,8.85822222222225,15.824,13.0933333333334,15.9266666666666,1.77422222222222,11.936
+mean,PRJNA15579,NA,NA,1,16.6505867014342,3.78031290743155,19.5834419817471,21.8826597131682,11.480443285528,19.0977835723598,5.45436766623207,33.1981747066493,26.27444589309,26.9393741851369,7.32855280312908,24.1786179921773,10.1975228161669,8.32268578878747,9.73272490221643,20.1675358539765,21.6988265971317,20.2979139504563,1.77835723598436,13.9406779661017
+mean,PRJNA165425,NA,NA,1,25.6383207750269,3.20452099031216,19.1103336921421,26.272874058127,14.6130247578041,25.3573735199139,7.43702906350914,23.4720129171152,22.1167922497309,36.3304628632939,9.33907427341227,15.2238966630786,14.6286329386437,13.694833153929,18.3509149623251,22.9305705059204,19.7395048439182,23.7922497308934,4.14693218514532,15.2039827771798
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+mean,PRJNA41955,NA,NA,1,24.8865823740328,4.44480090583128,20.0041517267409,24.0845442536328,16.5051896584261,24.6063408190224,6.60652953387431,25.0915267031516,24.6901302132478,32.4866956029439,9.86450273636535,19.2615587846764,13.4521607850538,12.7063596905076,16.5518022268353,22.6391772032459,20.9773542177769,22.8779014908473,4.84317795810529,16.7950556708813
+mean,PRJNA41965,NA,NA,1,29.0004206983593,4.11653344551956,16.4328986116954,21.0938157341186,14.0719394194363,23.7904922170804,5.71897349600337,19.7038283550694,20.7219183845183,31.4619267984855,8.12242322254943,12.8165755153555,14.2557846024401,10.7454774926378,16.2486327303323,19.9991586032815,16.6432477913336,22.8342448464451,3.80647875473285,9.10727808161548
+mean,PRJNA42541,NA,NA,1,28.0457581830327,4.88844355377422,17.1780227120908,21.0384101536406,11.6706746826987,23.8690714762859,5.60955243820975,17.4509018036072,15.4579158316633,31.5200400801604,8.74215096860387,10.4706078824315,12.8517034068136,12.6710086840347,16.4946559786239,17.3099532398129,17.2551770207081,22.2668670674683,3.4939879759519,10.8196392785571
+mean,PRJNA43469,NA,NA,1,24.7040320274521,4.48012582213326,19.4984272233343,24.7480697740921,16.9977123248499,24.8492993994853,6.45896482699457,25.5187303402917,23.8687446382614,34.1592793823277,9.38547326279668,17.613668859022,13.3122676579926,12.7752359164999,18.0780669144981,21.0346010866457,19.7843866171004,23.7331998856162,4.50185873605948,16.2490706319702
+mean,PRJNA46373,NA,NA,1,30.3820272572402,4.10988074957411,19.4463373083475,21.4041737649063,15.0494037478705,27.6379897785349,6.52683134582624,21.9557069846678,17.9246166950596,33.1946337308347,9.21933560477002,14.4667802385008,15.8211243611584,11.8790459965928,20.8317717206133,21.144804088586,20.2942930153322,24.7695911413969,4.29173764906303,14.0621805792163
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/chnosz -r 119
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