##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:STATegRa.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings STATegRa_1.42.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/STATegRa.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘STATegRa/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘STATegRa’ version ‘1.42.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘STATegRa’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
modelSelection,list-numeric-character: no visible binding for global
  variable ‘components’
modelSelection,list-numeric-character: no visible binding for global
  variable ‘mylabel’
plotVAF,caClass: no visible binding for global variable ‘comp’
plotVAF,caClass: no visible binding for global variable ‘VAF’
plotVAF,caClass: no visible binding for global variable ‘block’
selectCommonComps,list-numeric: no visible binding for global variable
  ‘comps’
selectCommonComps,list-numeric: no visible binding for global variable
  ‘block’
selectCommonComps,list-numeric: no visible binding for global variable
  ‘comp’
selectCommonComps,list-numeric: no visible binding for global variable
  ‘ratio’
Undefined global functions or variables:
  VAF block comp components comps mylabel ratio
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘STATEgRa_Example.omicsCLUST.R’
  Running ‘STATEgRa_Example.omicsPCA.R’
  Running ‘STATegRa_Example.omicsNPC.R’
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/STATegRa.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL STATegRa
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.4.3/site-library’
* installing *source* package ‘STATegRa’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (STATegRa)

R version 4.4.3 (2025-02-28) -- "Trophy Case"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("STATegRa")
Common components
[1] 2

Distinctive components
[[1]]
[1] 0

[[2]]
[1] 0

Common components
[1] 2

Distinctive components
[[1]]
[1] 1

[[2]]
[1] 1

Common components
[1] 2

Distinctive components
[[1]]
[1] 2

[[2]]
[1] 2



RUNIT TEST PROTOCOL -- Tue Mar 18 12:13:25 2025 
*********************************************** 
Number of test functions: 4 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
STATegRa RUnit Tests - 4 test functions, 0 errors, 0 failures
Number of test functions: 4 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: In rownames(pData) == colnames(exprs) :
  longer object length is not a multiple of shorter object length
2: In modelSelection(Input = list(B1, B2), Rmax = 4, fac.sel = "%accum",  :
  Rmax cannot be higher than the minimum of components selected for each block. Rmax fixed to: 2
3: In modelSelection(Input = list(B1, B2), Rmax = 4, fac.sel = "fixed.num",  :
  Rmax cannot be higher than the minimum of components selected for each block. Rmax fixed to: 3
> 
> proc.time()
   user  system elapsed 
  3.029   0.111   3.135 

R version 4.4.3 (2025-02-28) -- "Trophy Case"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> ###########################################
> ########### EXAMPLE OF THE OMICSCLUSTERING
> ###########################################
> require(STATegRa)
Loading required package: STATegRa
> 
> #############################################
> ## PART 1: CREATING a bioMap CLASS
> #############################################
> ####### This part creates or reads the map between features.
> ####### In the present example the map is downloaded from a resource.
> #######   then the class is created.
> 
> #load("../data/STATegRa_S2.rda")
> data(STATegRa_S2)
> 
> MAP.SYMBOL<-bioMap(name = "Symbol-miRNA",
+                 metadata =  list(type_v1="Gene",type_v2="miRNA",
+                                  source_database="targetscan.Hs.eg.db",
+                                  data_extraction="July2014"),
+                 map=mapdata)
> 
> 
> #############################################
> ## PART 2: CREATING a bioDist CLASS
> #############################################
> ##### In the second part given a set of main features and surrogate feautres,
> #####    the profile of the main features is computed through the surrogate features.
> 
> # Load Data
> data(STATegRa_S1)
>   #load("../data/STATegRa.S1.Rdata")
> 
> ## Create ExpressionSets
> #  source("../R/STATegRa_omicsPCA_classes_and_methods.R")
> # Block1 - Expression data
> mRNA.ds <- createOmicsExpressionSet(Data=Block1,pData=ed,pDataDescr=c("classname"))
> # Block2 - miRNA expression data
> miRNA.ds <- createOmicsExpressionSet(Data=Block2,pData=ed,pDataDescr=c("classname"))
> 
> # Create Gene-gene distance computed through miRNA data
> bioDistmiRNA<-bioDist(referenceFeatures = rownames(Block1),     
+              reference = "Var1",
+              mapping = MAP.SYMBOL,
+              surrogateData = miRNA.ds,  ### miRNA data
+              referenceData = mRNA.ds,  ### mRNA data
+              maxitems=2,
+              selectionRule="sd",
+              expfac=NULL,
+              aggregation = "sum",
+              distance = "spearman",
+              noMappingDist = 0,
+              filtering = NULL,
+              name = "mRNAbymiRNA")
> 
> require(Biobase)
Loading required package: Biobase
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table,
    tapply, union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

> 
> # Create Gene-gene distance through mRNA data
> bioDistmRNA<-bioDistclass(name = "mRNAbymRNA",
+                  distance = cor(t(exprs(mRNA.ds)),method="spearman"),
+                  map.name = "id",
+                  map.metadata = list(),
+                  params = list())
> 
> #############################################
> ## PART 3: CREATING a LISTOF WEIGTHED DISTANCES MATRICES: bioDistWList
> #############################################
> 
> bioDistList<-list(bioDistmRNA,bioDistmiRNA)
> weights<-matrix(0,4,2)
> weights[,1]<-c(0,0.33,0.67,1)
> weights[,2]<-c(1,0.67,0.33,0)#
> 
> bioDistWList<-bioDistW(referenceFeatures = rownames(Block1),
+                        bioDistList = bioDistList,
+                        weights=weights)
> length(bioDistWList)
[1] 4
> 
> #############################################
> ## PART 4: DEFINING THE STRENGTH OF ASSOCIATIONS IN GENERAL
> #############################################
> 
> bioDistWPlot(referenceFeatures = rownames(Block1) ,
+                listDistW = bioDistWList,
+                method.cor="spearman")
Warning messages:
1: In cor.test.default(getDist(listDistW[[i]])[referenceFeatures, referenceFeatures],  :
  Cannot compute exact p-value with ties
2: In cor.test.default(getDist(listDistW[[i]])[referenceFeatures, referenceFeatures],  :
  Cannot compute exact p-value with ties
3: In cor.test.default(getDist(listDistW[[i]])[referenceFeatures, referenceFeatures],  :
  Cannot compute exact p-value with ties
> 
> #############################################
> ## PART 5: DEFINING THE ASSOCIATIONS FOR A GIVEN GENE
> #############################################
> 
> ## IDH1
> 
> IDH1.F<-bioDistFeature(Feature = "IDH1" ,
+                        listDistW = bioDistWList,
+                        threshold.cor=0.7)
> bioDistFeaturePlot(data=IDH1.F)
> 
> ## PDGFRA
> 
> #PDGFRA.F<-bioDistFeature(Feature = "PDGFRA" ,
> #                       listDistW = bioDistWList,
> #                       threshold.cor=0.7)
> #bioDistFeaturePlot(data=PDGFRA.F,name="../vignettes/PDGFRA.png")
> 
> ## EGFR
> #EGFR.F<-bioDistFeature(Feature = "EGFR" ,
> #                         listDistW = bioDistWList,
> #                         threshold.cor=0.7)
> #bioDistFeaturePlot(data=EGFR.F,name="../vignettes/EGFR.png")
> 
> ## MGMT
> #MGMT.F<-bioDistFeature(Feature = "MGMT" ,
> #                         listDistW = bioDistWList,
> #                         threshold.cor=0.5)
> #bioDistFeaturePlot(data=MGMT.F,name="../vignettes/MGMT.png")
> 
> 
> 
> 
> 
> proc.time()
   user  system elapsed 
 56.591   0.297  56.941 

R version 4.4.3 (2025-02-28) -- "Trophy Case"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> rm(list = ls())
> require("STATegRa")
Loading required package: STATegRa
> # Load the data
> data("TCGA_BRCA_Batch_93")
> # Setting dataTypes
> dataTypes <- c("count", "count", "continuous")
> # Setting methods to combine pvalues
> combMethods = c("Fisher", "Liptak", "Tippett")
> # Setting number of permutations
> numPerms = 1000
> # Setting number of cores
> numCores = 1
> # Setting holistOmics to print out the steps that it performs.
> verbose = TRUE
> # Run holistOmics analysis.
> output <- omicsNPC(dataInput = TCGA_BRCA_Data, dataTypes = dataTypes, combMethods = combMethods, numPerms = numPerms, numCores = numCores, verbose = verbose)
Compute initial statistics on data
Building NULL distributions by permuting data
Compute pseudo p-values based on NULL distributions...
NPC p-values calculation...
> 
> proc.time()
   user  system elapsed 
 90.766   0.437  91.412 

R version 4.4.3 (2025-02-28) -- "Trophy Case"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> ###########################################
> ########### EXAMPLE OF THE OMICSPCA
> ###########################################
> require(STATegRa)
Loading required package: STATegRa
> 
> # g_legend (not exported by STATegRa any more)
> ## code from https://github.com/hadley/ggplot2/wiki/Share-a-legend-between-two-ggplot2-graphs
> g_legend<-function(a.gplot){
+     tmp <- ggplot_gtable(ggplot_build(a.gplot))
+     leg <- which(sapply(tmp$grobs, function(x) x$name) == "guide-box")
+     legend <- tmp$grobs[[leg]]
+     return(legend)}
> 
> #########################
> ## PART 1. Load data
> 
> ## Load data
> data(STATegRa_S3)
> 
> ls()
[1] "Block1.PCA" "Block2.PCA" "ed.PCA"     "g_legend"  
> 
> ## Create ExpressionSets
> # Block1 - Expression data
> B1 <- createOmicsExpressionSet(Data=Block1.PCA,pData=ed.PCA,pDataDescr=c("classname"))
> # Block2 - miRNA expression data
> B2 <- createOmicsExpressionSet(Data=Block2.PCA,pData=ed.PCA,pDataDescr=c("classname"))
> 
> #########################
> ## PART 2.  Model Selection
> 
> require(grid)
Loading required package: grid
> require(gridExtra)
Loading required package: gridExtra
> require(ggplot2)
Loading required package: ggplot2
> 
> ## Select the optimal components
> ms <- modelSelection(Input=list(B1,B2),Rmax=4,fac.sel="single%",varthreshold=0.03,center=TRUE,scale=TRUE,weight=TRUE)
Common components
[1] 2

Distinctive components
[[1]]
[1] 2

[[2]]
[1] 2

> 
> 
> #########################
> ## PART 3. Component Analysis
> 
> ## 3.1 Component analysis of the three methods
> discoRes <- omicsCompAnalysis(Input=list(B1,B2),Names=c("expr","mirna"),method="DISCOSCA",Rcommon=2,Rspecific=c(2,2),center=TRUE,
+                               scale=TRUE,weight=TRUE)
> jiveRes <- omicsCompAnalysis(Input=list(B1,B2),Names=c("expr","mirna"),method="JIVE",Rcommon=2,Rspecific=c(2,2),center=TRUE,
+                              scale=TRUE,weight=TRUE)
> o2plsRes <- omicsCompAnalysis(Input=list(B1,B2),Names=c("expr","mirna"),method="O2PLS",Rcommon=2,Rspecific=c(2,2),center=TRUE,
+                               scale=TRUE,weight=TRUE)
> 
> ## 3.2 Exploring scores structures
> 
> # Exploring DISCO-SCA scores structure
> discoRes@scores$common ## Common scores
                      1             2
sample1   -0.0781575567  0.0431547786
sample2    0.1192221298 -0.0294023154
sample3    0.0531408783  0.0746837624
sample4   -0.0292971867  0.0006032510
sample5   -0.0202090777 -0.0110455469
sample6   -0.1226088482 -0.1053492707
sample7   -0.1078931258  0.0322420187
sample8   -0.1782891266 -0.1449331069
sample9   -0.0468697298  0.0455171840
sample10   0.0036032631 -0.0420078434
sample11   0.0035566380  0.0566285329
sample12  -0.1006129652 -0.0641393614
sample13   0.1174412674 -0.0907475681
sample14  -0.0981203564 -0.0617763121
sample15  -0.0085337175  0.0086957326
sample16  -0.0783146884 -0.1581332733
sample17   0.1483610639 -0.0638580168
sample18   0.0963084427 -0.0556687120
sample19   0.0217243111  0.0720127780
sample20   0.0635634006  0.0779611057
sample21   0.0201843879 -0.1566382218
sample22  -0.0218273707  0.0764056668
sample23  -0.0852039110  0.0032763679
sample24   0.1287181216 -0.1924428217
sample25   0.0430575611  0.0456637277
sample26   0.1453899714 -0.0541459677
sample27   0.0197483753  0.1185593947
sample28   0.1025339341 -0.0650655834
sample29  -0.0706022337  0.0682934069
sample30   0.1295623079  0.0066679127
sample31  -0.1147449327 -0.1232726573
sample32   0.0374308268 -0.0380248383
sample33  -0.0599520659 -0.0136935011
sample34   0.0984199339 -0.0375363851
sample35   0.0543096457  0.0378036357
sample36  -0.1403628010  0.0343640824
sample37  -0.0228947563  0.0732692089
sample38   0.0222073152  0.0962567789
sample39   0.0941739205 -0.0215180825
sample40  -0.0643806957  0.0687722264
sample41   0.0327635070  0.1232187216
sample42   0.0500431642  0.0292513030
sample43   0.0184497217 -0.0233043874
sample44  -0.1487889593 -0.1171212605
sample45   0.1050778671 -0.1123141409
sample46   0.1151191711  0.1093996309
sample47   0.0962591583  0.0288418835
sample48  -0.0004832713  0.0310377764
sample49  -0.1135203998 -0.1213937334
sample50   0.0123550046  0.1740762790
sample51  -0.0550527521 -0.1258930035
sample52  -0.0499118571 -0.0728580337
sample53  -0.1119772715 -0.1588063426
sample54   0.0360055707 -0.0228585535
sample55  -0.0210418834 -0.0006750403
sample56   0.0434171429 -0.0633131194
sample57  -0.0197820809 -0.1150753254
sample58  -0.0030440695 -0.0326127107
sample59  -0.0500256673 -0.0129520001
sample60  -0.0184280068 -0.0136215808
sample61  -0.0150298948 -0.0635095732
sample62   0.0304758871  0.0201237466
sample63  -0.1102250180 -0.1285968362
sample64  -0.1552586863 -0.0971184834
sample65   0.0058503806 -0.0207102894
sample66   0.0025607412 -0.0424285244
sample67  -0.1546638600  0.0661580403
sample68  -0.0536374136  0.0923605339
sample69  -0.0640332931 -0.0082003497
sample70  -0.0163521623  0.0663227292
sample71   0.0102536175  0.1345964194
sample72   0.0654191847  0.0196037501
sample73   0.1048553312 -0.0220998999
sample74  -0.0123800488 -0.0586156204
sample75  -0.0392079689  0.0209726679
sample76  -0.0648954558  0.0524759399
sample77  -0.1172922652  0.0201199935
sample78   0.1463072503 -0.0708400791
sample79  -0.0265208864  0.1603423482
sample80  -0.0279739155  0.0214154333
sample81  -0.0079212121  0.0738494740
sample82   0.1544234640  0.0361450803
sample83   0.0494205546  0.0049940627
sample84   0.0259039708  0.0346590845
sample85  -0.1116487395  0.0031405586
sample86   0.1306479143  0.0377156886
sample87   0.0554777864  0.0459739677
sample88   0.0301626439 -0.0382206695
sample89   0.1016866186 -0.0694077541
sample90  -0.0086821603  0.0201323659
sample91  -0.1578629616  0.2097793139
sample92  -0.0170933559  0.1655934247
sample93   0.0979805148  0.0121500715
sample94  -0.0131486156  0.0114929572
sample95  -0.0315682447  0.0758916181
sample96  -0.0024125820  0.0470184348
sample97  -0.0634545790 -0.0270304142
sample98   0.0359372613  0.0135466919
sample99   0.1009167502 -0.1124713804
sample100 -0.0551754075 -0.0246501900
sample101  0.0080116104  0.1627406721
sample102  0.0046451030 -0.0095475726
sample103  0.0472520938  0.0940383715
sample104 -0.0198157495  0.0591146221
sample105  0.0400238957  0.0160948325
sample106  0.0923810091 -0.0369004129
sample107  0.1019372410 -0.0224967045
sample108  0.0877091523  0.0128849466
sample109 -0.0864820344  0.0901078630
sample110  0.1223116456  0.0096108078
sample111 -0.0257352457  0.0936279222
sample112  0.0765285929 -0.0270378809
sample113 -0.0258799925 -0.0377439420
sample114 -0.0021141025  0.0882039682
sample115 -0.0303455380  0.0723732629
sample116 -0.0780504548  0.0685160593
sample117 -0.0536894157  0.0912023156
sample118 -0.0666649921  0.0236260545
sample119 -0.1021872493  0.2325002836
sample120 -0.0750216334 -0.0243346241
sample121  0.0756937846 -0.0942969941
sample122  0.0259631963 -0.0731922425
sample123  0.1037844719  0.0369178992
sample124 -0.0611205230 -0.0421648423
sample125  0.0738472613 -0.0066944505
sample126 -0.0972919066 -0.0762697635
sample127 -0.0824699386  0.0096644590
sample128  0.1249411436 -0.0929254781
sample129  0.0734063782  0.0434314414
sample130  0.0003500295  0.0309857056
sample131 -0.0930184022 -0.0155969465
sample132 -0.0736220657 -0.0732973180
sample133  0.0498398353  0.0462455550
sample134 -0.1644872661 -0.0720046122
sample135  0.0752295095 -0.0003868614
sample136 -0.0227149863  0.0495470117
sample137 -0.0564721608  0.0288861583
sample138 -0.0255986513  0.0610929173
sample139 -0.0621218781 -0.0235857016
sample140  0.0604149040  0.0435533555
sample141 -0.0246743073 -0.0532630729
sample142  0.0409563777 -0.0316235165
sample143  0.0077356361  0.0476908549
sample144 -0.0173240995  0.0156785731
sample145 -0.0485467890 -0.1202738514
sample146 -0.0419649869  0.0811241678
sample147  0.0977304723  0.0274772426
sample148 -0.0368253370 -0.0803969768
sample149  0.0072864909  0.1533016348
sample150 -0.1020825523 -0.0624821667
sample151 -0.0305397200  0.0289335918
sample152  0.0533595222  0.0638334694
sample153  0.0891639149 -0.1799455343
sample154  0.0727554479  0.0834129991
sample155  0.0880665886  0.0220771272
sample156  0.0276558915  0.0326602349
sample157  0.1155031578 -0.0183635104
sample158  0.0281506722  0.0104912466
sample159 -0.0663233836 -0.0443810335
sample160  0.0302643997 -0.0404300677
sample161 -0.0114713014  0.0591081983
sample162  0.1337090900 -0.1398131372
sample163 -0.1330120853 -0.1688769444
sample164  0.0150338096 -0.0028376210
sample165 -0.0076518871  0.0164145468
sample166 -0.0367791571 -0.0630615148
sample167 -0.1111989794 -0.0030066250
sample168  0.0672982932 -0.0446267048
sample169  0.0413003660 -0.0224446084
> discoRes@scores$dist[[1]] ## Distinctive scores for Block 1
                      1             2
sample1    0.0420464497  0.0867866004
sample2    0.0820848916 -0.0410969025
sample3   -0.0155963595 -0.0195186326
sample4    0.1001342605 -0.0410776606
sample5    0.0153479212 -0.0253257764
sample6   -0.0340242430 -0.0408223286
sample7   -0.0722601508  0.0002324097
sample8    0.0457614878 -0.0370007033
sample9    0.0086217867  0.0820184485
sample10   0.0423629935 -0.0083917745
sample11  -0.0022591802  0.0787764127
sample12  -0.0322077494  0.1479823467
sample13   0.0293967114 -0.0306742958
sample14  -0.0337432866 -0.0367508278
sample15  -0.0815559540  0.1275614037
sample16  -0.0508336760  0.0540604470
sample17  -0.0062556869  0.0041024871
sample18  -0.0705602357 -0.0351053201
sample19   0.0476786025 -0.0509595559
sample20  -0.0523024729  0.0715514192
sample21   0.0119246207 -0.0376087120
sample22  -0.0724455456 -0.0095634748
sample23   0.0992529633  0.0134298738
sample24   0.1595259677  0.0728683843
sample25   0.0920662430 -0.0749749481
sample26   0.0595565846  0.0848973515
sample27  -0.0826573469 -0.0086747368
sample28   0.0384831792  0.0440972638
sample29  -0.0777738401  0.1735298685
sample30  -0.1229474131 -0.0819018213
sample31  -0.0579754246 -0.0238646724
sample32  -0.0970366812 -0.0111434924
sample33  -0.1017580348 -0.0630452370
sample34  -0.0637903510  0.0377936346
sample35  -0.0790002615 -0.0229732308
sample36  -0.1224933135 -0.1274968058
sample37  -0.1798846197 -0.1673447634
sample38  -0.0466390493  0.0888153266
sample39   0.0168694374  0.0421535998
sample40  -0.1756416739 -0.1526661970
sample41  -0.0042465479  0.0004924565
sample42   0.0447826537 -0.0651501495
sample43  -0.0482292629 -0.0253533436
sample44   0.1986815412 -0.0545754180
sample45   0.0741914860  0.0054714049
sample46  -0.0478858578 -0.0007080297
sample47  -0.0608215569  0.0481615565
sample48   0.1381465646  0.0578300724
sample49   0.0530626754 -0.1405523694
sample50   0.0173652378  0.1602386071
sample51  -0.0462460773  0.0303473154
sample52  -0.0279998767  0.0280387949
sample53  -0.0667503558  0.0237700303
sample54  -0.0121812494 -0.0521354880
sample55  -0.0182392383  0.0221326679
sample56   0.0001306790  0.0030909302
sample57  -0.0316578801  0.0530190744
sample58  -0.0393892052 -0.0297801706
sample59  -0.1278272089 -0.0546540320
sample60  -0.1486965545  0.1069142189
sample61  -0.0793069766  0.0569790594
sample62  -0.1172821044 -0.0149210940
sample63   0.0028809099  0.1300524141
sample64  -0.0237299092  0.1073288458
sample65   0.0126543217  0.0589810333
sample66   0.0468232418 -0.0771066705
sample67  -0.1494284991 -0.0769877057
sample68  -0.0978020937 -0.0577363626
sample69  -0.0403090379  0.0156038329
sample70  -0.0221595375  0.0315436648
sample71   0.0546334246 -0.0272395095
sample72  -0.1107500441 -0.0537331161
sample73  -0.0906756946  0.0579958060
sample74  -0.0586515100  0.0121417584
sample75  -0.0390511919  0.0349278293
sample76   0.0022940628 -0.1676560104
sample77   0.0232101530 -0.2067300992
sample78   0.0929807661 -0.0434928147
sample79   0.1619385520 -0.0378102837
sample80  -0.0680391865  0.1424656065
sample81   0.0530727932 -0.0358347800
sample82  -0.0266849245 -0.0577449061
sample83  -0.1517241723 -0.0448569802
sample84   0.0570944202 -0.0273808584
sample85  -0.1086272079 -0.1228130192
sample86  -0.0833890335 -0.0442924659
sample87  -0.0022039755 -0.0943908506
sample88   0.0078274902 -0.1140504542
sample89  -0.0611007941 -0.0094589266
sample90  -0.0022940965 -0.0936254876
sample91  -0.0433766291  0.3205972224
sample92   0.1815222495 -0.0334667081
sample93  -0.0267653225  0.0614425842
sample94  -0.0181900617  0.0605088191
sample95   0.0720316767 -0.0013040733
sample96   0.0559674371 -0.0118787272
sample97   0.0217420223  0.0195417154
sample98  -0.0379198487  0.0588352826
sample99   0.0792505013 -0.0151262541
sample100 -0.0222100973 -0.0023322886
sample101  0.0387089799  0.1224225088
sample102  0.2094625615 -0.0516421307
sample103 -0.0138554971  0.0301047646
sample104  0.0807949594 -0.0162712565
sample105  0.0520492081 -0.1229660471
sample106  0.0192641816 -0.0185235207
sample107 -0.0319014547  0.0405120629
sample108  0.0140674810  0.0163422297
sample109  0.1831859757  0.0613023284
sample110  0.0292782955 -0.0199846554
sample111  0.1423176818  0.0327351766
sample112 -0.0426314039 -0.0029086967
sample113  0.0771931026  0.0268742583
sample114  0.0241570823 -0.0184080724
sample115  0.1958958354  0.0460148166
sample116  0.1394438961 -0.0530793791
sample117  0.1672313862 -0.1386522317
sample118  0.0448332100 -0.0117618078
sample119  0.0910199898  0.2217435548
sample120  0.0331404478 -0.0057270403
sample121 -0.0307518802  0.1392506275
sample122  0.0839835845 -0.0291983786
sample123 -0.0239674390 -0.0642167365
sample124  0.0909175483  0.0130429937
sample125  0.0065362132 -0.1092631039
sample126 -0.0935274744  0.1368277032
sample127 -0.0035405150  0.0292755009
sample128  0.0660348305  0.1018575652
sample129 -0.0693670001 -0.0695430130
sample130 -0.0008516278 -0.0669705400
sample131 -0.0431012349  0.0174061103
sample132  0.0637087479  0.0029383381
sample133  0.0289465610 -0.0390817368
sample134 -0.0446143976  0.0456332423
sample135 -0.0712343641  0.0521627741
sample136 -0.0596317048  0.0197291796
sample137 -0.0793174749 -0.0380637139
sample138  0.0973506956 -0.0454210335
sample139 -0.0539867061 -0.1534331987
sample140 -0.0850870879  0.0955804596
sample141  0.0192722677 -0.0554446506
sample142  0.0672293495 -0.0461313207
sample143  0.0303707903 -0.0519258603
sample144  0.0089350971  0.0145815348
sample145  0.0638873711  0.0122268639
sample146 -0.0585920641  0.0063074998
sample147 -0.0894146271 -0.1124625627
sample148  0.0216437567 -0.0615962431
sample149  0.0515319659 -0.0839902984
sample150 -0.0568230364 -0.0124472604
sample151  0.0789514257 -0.0261824108
sample152  0.0330694940  0.1306444920
sample153  0.1752061165  0.1497755187
sample154 -0.0421487842 -0.0037017051
sample155 -0.0680198206  0.0095703634
sample156 -0.0388949214  0.1057558018
sample157 -0.0314765303  0.0561364703
sample158 -0.0329630014  0.0353943684
sample159  0.0398460439 -0.1007368356
sample160 -0.0424906752  0.0108493145
sample161  0.0888341251 -0.0679693003
sample162  0.0027567912  0.1237848301
sample163  0.0126225727  0.0725440897
sample164  0.0566787043 -0.0458318405
sample165  0.0315331738 -0.0236359640
sample166  0.0612107839 -0.0425224941
sample167 -0.0142729582  0.0179307025
sample168  0.0169541958 -0.0769614902
sample169 -0.0675063901  0.0131499209
> discoRes@scores$dist[[2]] ## Distinctive scores for Block 2
                     1             2
sample1   -0.001233163  1.635716e-01
sample2   -0.072435315  6.022108e-03
sample3   -0.018845995  1.080029e-01
sample4    0.039014317 -3.106707e-04
sample5    0.177481065  2.996428e-02
sample6   -0.045144642  3.455897e-02
sample7   -0.022646354  7.019233e-03
sample8   -0.103368448  9.857920e-03
sample9    0.135001417 -8.979113e-02
sample10   0.125988447  5.097935e-02
sample11   0.097979088 -7.086566e-02
sample12  -0.086302096  8.620322e-02
sample13  -0.138140181 -1.827998e-01
sample14  -0.061507472  2.642808e-02
sample15   0.038160055  3.101603e-02
sample16  -0.004877935 -1.271042e-03
sample17  -0.078848318  1.547605e-02
sample18  -0.088418948  3.795477e-02
sample19   0.070304354  1.084003e-01
sample20  -0.002558143 -7.975967e-02
sample21   0.094159673  4.126890e-02
sample22  -0.055027091  7.806620e-02
sample23   0.067949286  4.102075e-02
sample24  -0.131096932 -1.649283e-01
sample25   0.011358360  4.426899e-02
sample26  -0.140294886 -2.016461e-02
sample27   0.026156596 -1.589924e-03
sample28  -0.072420075 -5.850512e-02
sample29  -0.033005485 -2.062047e-03
sample30  -0.022875037  2.015346e-02
sample31  -0.063507037  6.670368e-02
sample32   0.068510000  4.955247e-02
sample33  -0.077776493  1.272070e-01
sample34   0.015784209  3.024311e-02
sample35  -0.052962802 -1.500981e-01
sample36   0.007090785 -2.025320e-01
sample37  -0.044241196 -1.802109e-01
sample38  -0.078150843  3.676301e-02
sample39   0.012033010  3.388883e-02
sample40  -0.047328398 -1.471581e-01
sample41   0.022819214  2.673460e-02
sample42  -0.024536183  7.960877e-02
sample43   0.103636203  8.229577e-02
sample44  -0.101223467 -7.049246e-02
sample45   0.001372679  2.451065e-02
sample46  -0.055850651 -2.948555e-03
sample47  -0.038047876 -4.554235e-02
sample48   0.078434049 -4.888894e-02
sample49  -0.060516799  1.162468e-02
sample50   0.053008285  2.737817e-02
sample51   0.151464537 -5.678262e-02
sample52   0.186093600 -1.246711e-01
sample53  -0.006417966  2.701058e-02
sample54   0.069703758  2.308412e-02
sample55   0.163357769 -1.366433e-02
sample56   0.101148402 -4.682135e-02
sample57   0.173037440 -1.609594e-01
sample58  -0.007138489  1.666951e-02
sample59  -0.003045853 -3.005373e-02
sample60   0.021584206 -2.665887e-01
sample61   0.151058530 -1.002384e-01
sample62  -0.092553163  4.845731e-02
sample63  -0.059631538  4.137106e-02
sample64  -0.044922726  2.600952e-03
sample65   0.093938227  4.406949e-02
sample66   0.106339779  5.710076e-02
sample67  -0.020158098 -2.361746e-01
sample68   0.003720830 -2.418539e-02
sample69  -0.064516199  1.155618e-01
sample70  -0.101343975  1.351780e-01
sample71  -0.001646613  2.976775e-02
sample72   0.032889536  2.835774e-02
sample73   0.027508038  5.148153e-02
sample74   0.134171839  7.895302e-02
sample75   0.095157662  3.943149e-02
sample76  -0.086471998 -3.035052e-02
sample77  -0.103574950  2.545326e-02
sample78  -0.157564780 -4.939478e-02
sample79   0.018913836 -4.874690e-02
sample80   0.138414273 -4.313593e-05
sample81  -0.011884666  6.357909e-02
sample82  -0.167530666 -3.533967e-02
sample83  -0.006567120  7.812500e-02
sample84   0.148689068  3.109095e-02
sample85  -0.053272042 -7.417986e-02
sample86  -0.113847496  1.822573e-05
sample87   0.043286592 -6.080499e-02
sample88   0.043345119 -1.402486e-01
sample89   0.033120482  1.395427e-02
sample90  -0.060741346  8.610386e-02
sample91  -0.056626392 -1.303769e-01
sample92  -0.035958072 -1.061605e-01
sample93  -0.043364646  4.443610e-02
sample94  -0.047729212  1.059571e-01
sample95  -0.024959592  3.980510e-02
sample96   0.003521761  9.293931e-02
sample97  -0.006605195  1.527234e-01
sample98   0.002036706  5.579516e-02
sample99  -0.088662162  3.728370e-02
sample100 -0.109125960  3.560402e-02
sample101 -0.073972388  4.317888e-02
sample102  0.057445582  2.784081e-02
sample103  0.014273370 -9.706331e-03
sample104  0.071039558 -4.068331e-02
sample105  0.098082997  3.452995e-02
sample106 -0.025426047 -3.628934e-02
sample107 -0.016065501  9.173398e-02
sample108 -0.020098830  2.379699e-02
sample109 -0.038978191 -1.692313e-02
sample110 -0.032630524 -2.988088e-02
sample111  0.067693597  6.038248e-02
sample112  0.016788351 -5.336924e-03
sample113  0.096921401  2.757700e-02
sample114 -0.002639798  9.209103e-02
sample115 -0.030804952 -1.603746e-02
sample116 -0.124030640 -1.272998e-01
sample117  0.033472867 -5.392664e-02
sample118 -0.103715217 -6.252439e-02
sample119 -0.106417070 -1.196217e-01
sample120 -0.077135766  1.004935e-01
sample121 -0.012935229 -3.181916e-02
sample122  0.084748765  5.568460e-02
sample123 -0.004133554 -7.693543e-03
sample124 -0.058346212  8.396473e-02
sample125  0.063484328  5.232567e-02
sample126 -0.066258209  1.091730e-01
sample127 -0.086502560  1.094173e-01
sample128 -0.062782194  1.471090e-02
sample129 -0.033627462  4.007777e-02
sample130 -0.029351810  8.046087e-02
sample131 -0.046919681  2.209395e-03
sample132 -0.024174554  1.248608e-01
sample133  0.090730379 -1.466698e-02
sample134 -0.035084125 -7.539660e-02
sample135  0.000133485 -9.185806e-03
sample136 -0.033587483  9.860184e-02
sample137 -0.064014730  7.554374e-02
sample138  0.006096407  1.742782e-02
sample139 -0.059208279 -5.615005e-02
sample140  0.042798855  1.099468e-02
sample141  0.061879333  9.301100e-02
sample142  0.089855255 -3.573327e-02
sample143  0.081739103 -8.880528e-02
sample144  0.078775448  3.821395e-02
sample145  0.108581955 -1.569461e-01
sample146 -0.058955506  4.373240e-02
sample147 -0.049532796 -7.278036e-03
sample148  0.116159053 -9.078162e-03
sample149 -0.012157557 -7.788460e-02
sample150 -0.031451199 -3.520220e-02
sample151  0.057538097  1.945391e-02
sample152 -0.049454039 -7.025565e-02
sample153 -0.094133842 -2.153271e-01
sample154 -0.033592889 -2.078822e-02
sample155  0.069045902  2.780363e-02
sample156  0.103990229  6.292489e-02
sample157 -0.040864584 -8.065529e-03
sample158  0.101810632 -7.817016e-03
sample159 -0.028173249  1.207258e-02
sample160  0.164305287 -2.977818e-03
sample161  0.037433007 -8.524589e-02
sample162 -0.080453821 -8.349639e-02
sample163 -0.074323231  1.406343e-02
sample164  0.120880432  2.139522e-02
sample165  0.160811596 -2.025160e-02
sample166 -0.042594786  2.660798e-02
sample167 -0.022684951  4.464259e-02
sample168 -0.018073733  7.471387e-04
sample169  0.019078018 -2.645426e-02
> # Exploring O2PLS scores structure
> o2plsRes@scores$common[[1]] ## Common scores for Block 1
                   [,1]          [,2]
sample1   -0.0572060227 -1.729087e-02
sample2    0.0875245208  1.112588e-02
sample3    0.0403482602 -3.168994e-02
sample4   -0.0218345996  4.052760e-06
sample5   -0.0150905011  4.795041e-03
sample6   -0.0924362933  4.511003e-02
sample7   -0.0793066751 -1.243823e-02
sample8   -0.1342997187  6.215220e-02
sample9   -0.0338886944 -1.854401e-02
sample10   0.0020547173  1.749421e-02
sample11   0.0037275602 -2.364116e-02
sample12  -0.0753094533  2.772698e-02
sample13   0.0856160091  3.679963e-02
sample14  -0.0737457307  2.668452e-02
sample15  -0.0062111746 -3.554864e-03
sample16  -0.0602355268  6.675115e-02
sample17   0.1086768843  2.524534e-02
sample18   0.0702999472  2.231671e-02
sample19   0.0173785882 -3.024846e-02
sample20   0.0484173812 -3.310904e-02
sample21   0.0124657042  6.517144e-02
sample22  -0.0140989936 -3.159137e-02
sample23  -0.0627028403 -5.393710e-04
sample24   0.0919972100  7.909297e-02
sample25   0.0326998483 -1.945206e-02
sample26   0.1064741246  2.120849e-02
sample27   0.0166058995 -4.964993e-02
sample28   0.0743504770  2.614211e-02
sample29  -0.0511008491 -2.782647e-02
sample30   0.0962250842 -3.974893e-03
sample31  -0.0869563008  5.250819e-02
sample32   0.0271858919  1.552005e-02
sample33  -0.0448364581  6.243160e-03
sample34   0.0718415218  1.469396e-02
sample35   0.0403086451 -1.632629e-02
sample36  -0.1036402827 -1.304320e-02
sample37  -0.0159385744 -3.036525e-02
sample38   0.0182198369 -4.034805e-02
sample39   0.0690363619  8.058350e-03
sample40  -0.0467312750 -2.810325e-02
sample41   0.0263674438 -5.171216e-02
sample42   0.0374578960 -1.268634e-02
sample43   0.0132336869  9.536642e-03
sample44  -0.1119154428  5.028683e-02
sample45   0.0759639367  4.587903e-02
sample46   0.0871885519 -4.670385e-02
sample47   0.0721490571 -1.288540e-02
sample48   0.0005086144 -1.290565e-02
sample49  -0.0858177028  5.173760e-02
sample50   0.0118992665 -7.276215e-02
sample51  -0.0426446855  5.306205e-02
sample52  -0.0381605826  3.086785e-02
sample53  -0.0855757630  6.730043e-02
sample54   0.0261723092  9.184260e-03
sample55  -0.0156418304  4.682404e-04
sample56   0.0307831193  2.597550e-02
sample57  -0.0157242103  4.829381e-02
sample58  -0.0031174404  1.359898e-02
sample59  -0.0373001859  5.868397e-03
sample60  -0.0142609099  5.831654e-03
sample61  -0.0122255144  2.663579e-02
sample62   0.0228002942 -8.692265e-03
sample63  -0.0833127581  5.473229e-02
sample64  -0.1166548159  4.196500e-02
sample65   0.0038808902  8.568590e-03
sample66   0.0011561811  1.766612e-02
sample67  -0.1129311062 -2.608702e-02
sample68  -0.0382526429 -3.804045e-02
sample69  -0.0476502440  4.003241e-03
sample70  -0.0110329882 -2.752719e-02
sample71   0.0096850282 -5.627056e-02
sample72   0.0487124704 -8.800131e-03
sample73   0.0773058132  8.239864e-03
sample74  -0.0102488176  2.454957e-02
sample75  -0.0286613976 -8.387293e-03
sample76  -0.0472655595 -2.129315e-02
sample77  -0.0865043074 -7.296820e-03
sample78   0.1070293698  2.818346e-02
sample79  -0.0165060681 -6.659721e-02
sample80  -0.0206765949 -8.712112e-03
sample81  -0.0050943615 -3.079175e-02
sample82   0.1153622361 -1.647054e-02
sample83   0.0367979217 -2.538114e-03
sample84   0.0199463070 -1.468961e-02
sample85  -0.0827122185 -2.709824e-04
sample86   0.0969487314 -1.699897e-02
sample87   0.0421957457 -1.965953e-02
sample88   0.0215934743  1.566050e-02
sample89   0.0751559502  2.811652e-02
sample90  -0.0057328000 -8.283795e-03
sample91  -0.1134005268 -8.603522e-02
sample92  -0.0101689918 -6.894992e-02
sample93   0.0725967502 -6.003176e-03
sample94  -0.0096878852 -4.693081e-03
sample95  -0.0223502239 -3.139636e-02
sample96  -0.0013232863 -1.963604e-02
sample97  -0.0476541710  1.183660e-02
sample98   0.0269546160 -5.978398e-03
sample99   0.0728179461  4.597884e-02
sample100 -0.0413398038  1.079347e-02
sample101  0.0087536994 -6.796076e-02
sample102  0.0032509529  3.932612e-03
sample103  0.0360342395 -3.973263e-02
sample104 -0.0141722563 -2.453107e-02
sample105  0.0294940465 -7.140722e-03
sample106  0.0686472054  1.462895e-02
sample107  0.0748635927  8.401339e-03
sample108  0.0650175850 -6.211942e-03
sample109 -0.0628017242 -3.681224e-02
sample110  0.0905513691 -5.169053e-03
sample111 -0.0176679473 -3.884777e-02
sample112  0.0570870472  1.066018e-02
sample113 -0.0200110554  1.596044e-02
sample114 -0.0001474542 -3.679272e-02
sample115 -0.0213333038 -2.991667e-02
sample116 -0.0567675453 -2.785636e-02
sample117 -0.0379865990 -3.752078e-02
sample118 -0.0484878786 -9.173691e-03
sample119 -0.0713511831 -9.598634e-02
sample120 -0.0555093586  1.089843e-02
sample121  0.0542443861  3.861344e-02
sample122  0.0178575357  3.027138e-02
sample123  0.0775020581 -1.636852e-02
sample124 -0.0460701050  1.814758e-02
sample125  0.0543846585  2.075898e-03
sample126 -0.0729417144  3.276659e-02
sample127 -0.0609509157 -3.270814e-03
sample128  0.0908136899  3.758801e-02
sample129  0.0552445878 -1.879062e-02
sample130  0.0007128089 -1.294308e-02
sample131 -0.0693311345  7.357082e-03
sample132 -0.0556565156  3.126995e-02
sample133  0.0375870104 -1.977240e-02
sample134 -0.1229130924  3.159495e-02
sample135  0.0555550315 -5.563250e-04
sample136 -0.0159768414 -2.046339e-02
sample137 -0.0412337694 -1.151652e-02
sample138 -0.0180604476 -2.526505e-02
sample139 -0.0465649201  1.040683e-02
sample140  0.0452288969 -1.876279e-02
sample141 -0.0189142561  2.247042e-02
sample142  0.0297545566  1.280524e-02
sample143  0.0064292003 -1.997706e-02
sample144 -0.0124284903 -6.369733e-03
sample145 -0.0377141491  5.066743e-02
sample146 -0.0296240067 -3.344465e-02
sample147  0.0726083535 -1.239968e-02
sample148 -0.0284795794  3.389732e-02
sample149  0.0082261455 -6.399305e-02
sample150 -0.0765013197  2.704021e-02
sample151 -0.0220567356 -1.178159e-02
sample152  0.0403422737 -2.714879e-02
sample153  0.0629117719  7.425085e-02
sample154  0.0551622927 -3.548984e-02
sample155  0.0654439133 -1.005306e-02
sample156  0.0209310714 -1.390213e-02
sample157  0.0851522597  6.577150e-03
sample158  0.0208354599 -4.663078e-03
sample159 -0.0498794349  1.913257e-02
sample160  0.0216074437  1.656579e-02
sample161 -0.0075742328 -2.455676e-02
sample162  0.0963663017  5.705881e-02
sample163 -0.1009542191  7.174224e-02
sample164  0.0109881996  1.026806e-03
sample165 -0.0053146157 -6.772855e-03
sample166 -0.0275757357  2.673084e-02
sample167 -0.0825048036  2.278863e-03
sample168  0.0486147429  1.793843e-02
sample169  0.0302506727  8.984253e-03
> o2plsRes@scores$common[[2]] ## Common scores for Block 2
                   [,1]          [,2]
sample1   -0.0621842115 -1.364509e-02
sample2    0.0944623785  9.720892e-03
sample3    0.0406196267 -2.236338e-02
sample4   -0.0229316496 -3.932487e-04
sample5   -0.0157330047  3.231033e-03
sample6   -0.0945794025  3.120720e-02
sample7   -0.0854427118 -1.052880e-02
sample8   -0.1376625920  4.286608e-02
sample9   -0.0377115311 -1.415134e-02
sample10   0.0035244506  1.280825e-02
sample11   0.0016639987 -1.717895e-02
sample12  -0.0781403168  1.884368e-02
sample13   0.0938400516  2.838858e-02
sample14  -0.0759839772  1.810989e-02
sample15  -0.0068340837 -2.705361e-03
sample16  -0.0590150849  4.757848e-02
sample17   0.1178805097  2.040526e-02
sample18   0.0767858320  1.756604e-02
sample19   0.0157112113 -2.172867e-02
sample20   0.0485318300 -2.327033e-02
sample21   0.0185928176  4.777095e-02
sample22  -0.0191358702 -2.329775e-02
sample23  -0.0672994194 -1.535656e-03
sample24   0.1047476642  5.935707e-02
sample25   0.0329844953 -1.358036e-02
sample26   0.1154952052  1.741529e-02
sample27   0.0133849853 -3.590922e-02
sample28   0.0821554039  2.042376e-02
sample29  -0.0567643690 -2.123848e-02
sample30   0.1016073931 -1.134728e-03
sample31  -0.0880396372  3.670548e-02
sample32   0.0300363338  1.182406e-02
sample33  -0.0467252272  3.739254e-03
sample34   0.0783666394  1.203777e-02
sample35   0.0424227097 -1.118559e-02
sample36  -0.1107646166 -1.143464e-02
sample37  -0.0191667664 -2.246060e-02
sample38   0.0155968095 -2.909621e-02
sample39   0.0746847148  7.148218e-03
sample40  -0.0517028178 -2.137267e-02
sample41   0.0234979494 -3.723018e-02
sample42   0.0388797356 -8.557228e-03
sample43   0.0149555568  7.210002e-03
sample44  -0.1150305613  3.461805e-02
sample45   0.0846146236  3.486020e-02
sample46   0.0884426404 -3.246853e-02
sample47   0.0748644971 -8.083045e-03
sample48  -0.0012033198 -9.403647e-03
sample49  -0.0872662737  3.616245e-02
sample50   0.0066941314 -5.284863e-02
sample51  -0.0411777630  3.791830e-02
sample52  -0.0379355780  2.180834e-02
sample53  -0.0851639886  4.751761e-02
sample54   0.0288006248  7.184424e-03
sample55  -0.0164920835  5.919925e-05
sample56   0.0355115616  1.951043e-02
sample57  -0.0141146068  3.492409e-02
sample58  -0.0015636132  9.862883e-03
sample59  -0.0390656483  3.590929e-03
sample60  -0.0139454780  3.963030e-03
sample61  -0.0106410274  1.919705e-02
sample62   0.0236748439 -5.922677e-03
sample63  -0.0846790877  3.839102e-02
sample64  -0.1202581015  2.846469e-02
sample65   0.0050548584  6.328644e-03
sample66   0.0028013072  1.291807e-02
sample67  -0.1231623009 -2.112565e-02
sample68  -0.0437782161 -2.845072e-02
sample69  -0.0501199692  2.053469e-03
sample70  -0.0140278645 -2.027157e-02
sample71   0.0057489505 -4.085977e-02
sample72   0.0511212704 -5.522408e-03
sample73   0.0828141409  7.431582e-03
sample74  -0.0085959456  1.772951e-02
sample75  -0.0312180394 -6.636869e-03
sample76  -0.0519051781 -1.640191e-02
sample77  -0.0925924762 -6.907800e-03
sample78   0.1163971046  2.251122e-02
sample79  -0.0240906926 -4.887766e-02
sample80  -0.0221327065 -6.730703e-03
sample81  -0.0072114968 -2.254399e-02
sample82   0.1204416674 -9.907422e-03
sample83   0.0386739485 -1.171663e-03
sample84   0.0195988488 -1.033806e-02
sample85  -0.0877680171 -1.725057e-03
sample86   0.1023541048 -1.062501e-02
sample87   0.0425213089 -1.356865e-02
sample88   0.0244788514  1.180820e-02
sample89   0.0804276691  2.188588e-02
sample90  -0.0074639871 -6.140721e-03
sample91  -0.1278832404 -6.485140e-02
sample92  -0.0162199697 -5.048358e-02
sample93   0.0769344893 -3.045135e-03
sample94  -0.0104345587 -3.593172e-03
sample95  -0.0260058453 -2.330475e-02
sample96  -0.0025018700 -1.433516e-02
sample97  -0.0492358305  7.774183e-03
sample98   0.0279220220 -3.862141e-03
sample99   0.0813921923  3.487339e-02
sample100 -0.0428797405  7.112807e-03
sample101  0.0032855240 -4.940743e-02
sample102  0.0038439317  2.938008e-03
sample103  0.0358511139 -2.831881e-02
sample104 -0.0162784000 -1.815061e-02
sample105  0.0314853405 -4.656633e-03
sample106  0.0726456731  1.192390e-02
sample107  0.0807342975  7.508627e-03
sample108  0.0688338003 -3.336161e-03
sample109 -0.0694151950 -2.800146e-02
sample110  0.0961218924 -2.111997e-03
sample111 -0.0217900036 -2.864702e-02
sample112  0.0599954082  8.820317e-03
sample113 -0.0195006577  1.128215e-02
sample114 -0.0032126533 -2.682851e-02
sample115 -0.0251101087 -2.221077e-02
sample116 -0.0625141551 -2.137258e-02
sample117 -0.0440473375 -2.806256e-02
sample118 -0.0532042630 -7.590494e-03
sample119 -0.0848603028 -7.133574e-02
sample120 -0.0588832131  6.937326e-03
sample121  0.0613899126  2.915307e-02
sample122  0.0218424338  2.241775e-02
sample123  0.0809008460 -1.051759e-02
sample124 -0.0472109313  1.239887e-02
sample125  0.0583180947  2.521167e-03
sample126 -0.0753941872  2.256455e-02
sample127 -0.0649774209 -3.496964e-03
sample128  0.1000212216  2.908091e-02
sample129  0.0568033049 -1.269016e-02
sample130 -0.0002370832 -9.419675e-03
sample131 -0.0727030877  4.091672e-03
sample132 -0.0566219024  2.179861e-02
sample133  0.0384172955 -1.372840e-02
sample134 -0.1280862736  2.077912e-02
sample135  0.0592633273  6.106685e-04
sample136 -0.0187635410 -1.521173e-02
sample137 -0.0449958970 -9.152840e-03
sample138 -0.0211348699 -1.875415e-02
sample139 -0.0482882861  6.729304e-03
sample140  0.0468926306 -1.285498e-02
sample141 -0.0186248693  1.605439e-02
sample142  0.0328031246  9.887746e-03
sample143  0.0052919839 -1.445666e-02
sample144 -0.0140067923 -4.867248e-03
sample145 -0.0361804310  3.625323e-02
sample146 -0.0345286735 -2.493652e-02
sample147  0.0765025670 -7.714769e-03
sample148 -0.0276016641  2.420589e-02
sample149  0.0027545308 -4.653007e-02
sample150 -0.0792296010  1.831289e-02
sample151 -0.0245894512 -8.991738e-03
sample152  0.0409796547 -1.907063e-02
sample153  0.0734301757  5.528780e-02
sample154  0.0557740684 -2.487723e-02
sample155  0.0689436560 -6.127635e-03
sample156  0.0212272938 -9.747423e-03
sample157  0.0911931194  6.355708e-03
sample158  0.0220840645 -3.016357e-03
sample159 -0.0513244242  1.304175e-02
sample160  0.0246213576  1.248444e-02
sample161 -0.0100369130 -1.805391e-02
sample162  0.1078802043  4.337260e-02
sample163 -0.1017965082  5.047171e-02
sample164  0.0119430799  9.593002e-04
sample165 -0.0063708014 -5.032148e-03
sample166 -0.0283181180  1.899222e-02
sample167 -0.0872832229  1.516582e-04
sample168  0.0540714512  1.397701e-02
sample169  0.0328432652  7.104347e-03
> o2plsRes@scores$dist[[1]] ## Distinctive scores for Block 1
                   [,1]          [,2]
sample1    0.0133684846  2.195848e-02
sample2    0.0254157197 -1.058416e-02
sample3   -0.0049551479 -4.840017e-03
sample4    0.0310390570 -1.063929e-02
sample5    0.0046941318 -6.488426e-03
sample6   -0.0107406753 -1.026702e-02
sample7   -0.0225157631  2.624712e-04
sample8    0.0141320952 -9.505821e-03
sample9    0.0029681280  2.078210e-02
sample10   0.0131729174 -2.275042e-03
sample11  -0.0004164298  1.994019e-02
sample12  -0.0095211620  3.759883e-02
sample13   0.0091018604 -7.953956e-03
sample14  -0.0106557524 -9.181659e-03
sample15  -0.0249924121  3.262724e-02
sample16  -0.0156216400  1.375700e-02
sample17  -0.0019382446  1.073994e-03
sample18  -0.0221072481 -8.703592e-03
sample19   0.0146917619 -1.311712e-02
sample20  -0.0160353760  1.826290e-02
sample21   0.0035947899 -9.616341e-03
sample22  -0.0225060762 -2.532589e-03
sample23   0.0310000683  3.033060e-03
sample24   0.0499544372  1.809450e-02
sample25   0.0284442301 -1.932558e-02
sample26   0.0188220043  2.146985e-02
sample27  -0.0257763219 -1.999228e-03
sample28   0.0120888648  1.125834e-02
sample29  -0.0236482520  4.426726e-02
sample30  -0.0385486305 -2.055935e-02
sample31  -0.0181539336 -5.877838e-03
sample32  -0.0302630460 -2.607192e-03
sample33  -0.0319565715 -1.562628e-02
sample34  -0.0197970124  9.906813e-03
sample35  -0.0247412713 -5.434440e-03
sample36  -0.0386259060 -3.190394e-02
sample37  -0.0566199273 -4.192574e-02
sample38  -0.0142060273  2.259644e-02
sample39   0.0053589035  1.076485e-02
sample40  -0.0552546493 -3.819896e-02
sample41  -0.0013089975  9.278818e-05
sample42   0.0137252142 -1.664652e-02
sample43  -0.0151259626 -6.290953e-03
sample44   0.0617391754 -1.442883e-02
sample45   0.0231410886  1.163143e-03
sample46  -0.0148898209 -1.384176e-04
sample47  -0.0187252536  1.221690e-02
sample48   0.0432839432  1.416671e-02
sample49   0.0160818605 -3.588745e-02
sample50   0.0059333545  4.067003e-02
sample51  -0.0142914866  7.776270e-03
sample52  -0.0086339952  7.208917e-03
sample53  -0.0207386980  6.272432e-03
sample54  -0.0039856719 -1.316934e-02
sample55  -0.0056217017  5.692315e-03
sample56   0.0000123292  8.978290e-04
sample57  -0.0095805555  1.324253e-02
sample58  -0.0124160295 -7.326376e-03
sample59  -0.0400195442 -1.349736e-02
sample60  -0.0460063358  2.770091e-02
sample61  -0.0245266456  1.470710e-02
sample62  -0.0366022783 -3.437352e-03
sample63   0.0013742171  3.288796e-02
sample64  -0.0070599859  2.739588e-02
sample65   0.0041201911  1.498268e-02
sample66   0.0143173351 -1.968812e-02
sample67  -0.0467477531 -1.929938e-02
sample68  -0.0306751978 -1.436184e-02
sample69  -0.0125317217  4.130407e-03
sample70  -0.0068071487  8.080857e-03
sample71   0.0169170264 -7.027348e-03
sample72  -0.0346909749 -1.333770e-02
sample73  -0.0280506153  1.493843e-02
sample74  -0.0182611498  3.294697e-03
sample75  -0.0120563964  8.974612e-03
sample76   0.0001437236 -4.253184e-02
sample77   0.0065330299 -5.252886e-02
sample78   0.0288278141 -1.127782e-02
sample79   0.0503961481 -1.023318e-02
sample80  -0.0207693429  3.648391e-02
sample81   0.0163562768 -9.074596e-03
sample82  -0.0084317129 -1.478976e-02
sample83  -0.0474097918 -1.103126e-02
sample84   0.0177181395 -7.191197e-03
sample85  -0.0342718548 -3.082360e-02
sample86  -0.0261671791 -1.089491e-02
sample87  -0.0009486358 -2.411514e-02
sample88   0.0020528931 -2.894615e-02
sample89  -0.0189361111 -2.638639e-03
sample90  -0.0009863658 -2.390075e-02
sample91  -0.0124352695  8.153234e-02
sample92   0.0564264106 -8.909537e-03
sample93  -0.0081461774  1.570851e-02
sample94  -0.0054896581  1.547251e-02
sample95   0.0224073150 -4.374348e-04
sample96   0.0173528924 -3.050441e-03
sample97   0.0067948115  5.008237e-03
sample98  -0.0116030825  1.498764e-02
sample99   0.0246422688 -4.054795e-03
sample100 -0.0069420745 -4.846343e-04
sample101  0.0124923691  3.091503e-02
sample102  0.0650835386 -1.367400e-02
sample103 -0.0042741828  7.855985e-03
sample104  0.0250591040 -4.171938e-03
sample105  0.0157516368 -3.121990e-02
sample106  0.0060593853 -5.101693e-03
sample107 -0.0098329626  1.044506e-02
sample108  0.0044269853  4.142036e-03
sample109  0.0572473486  1.517542e-02
sample110  0.0090474827 -5.119868e-03
sample111  0.0444263015  7.983232e-03
sample112 -0.0131765484 -9.696342e-04
sample113  0.0241047399  6.706740e-03
sample114  0.0074558775 -4.728652e-03
sample115  0.0611851433  1.117210e-02
sample116  0.0432646951 -1.380556e-02
sample117  0.0516750066 -3.575617e-02
sample118  0.0139942100 -3.279138e-03
sample119  0.0291722987  5.587946e-02
sample120  0.0103515853 -1.690016e-03
sample121 -0.0091396331  3.552116e-02
sample122  0.0260431679 -7.583975e-03
sample123 -0.0076666389 -1.628489e-02
sample124  0.0283466326  3.127845e-03
sample125  0.0016472378 -2.770692e-02
sample126 -0.0286529417  3.489336e-02
sample127 -0.0010224500  7.483214e-03
sample128  0.0209049296  2.572016e-02
sample129 -0.0218184878 -1.755347e-02
sample130 -0.0005009620 -1.697978e-02
sample131 -0.0134032968  4.637390e-03
sample132  0.0198526786  5.723983e-04
sample133  0.0088812957 -9.988115e-03
sample134 -0.0137484514  1.172591e-02
sample135 -0.0220314568  1.347465e-02
sample136 -0.0185173353  5.168079e-03
sample137 -0.0248352123 -9.472788e-03
sample138  0.0301635767 -1.175283e-02
sample139 -0.0173576929 -3.872592e-02
sample140 -0.0262157762  2.456863e-02
sample141  0.0058369763 -1.420854e-02
sample142  0.0207886071 -1.188764e-02
sample143  0.0092832598 -1.324238e-02
sample144  0.0028442140  3.627979e-03
sample145  0.0199749569  2.862202e-03
sample146 -0.0182236697  1.726556e-03
sample147 -0.0282519995 -2.825595e-02
sample148  0.0065435868 -1.572917e-02
sample149  0.0158233820 -2.159451e-02
sample150 -0.0177383738 -3.020633e-03
sample151  0.0245166984 -6.888241e-03
sample152  0.0107259913  3.314630e-02
sample153  0.0550963965  3.758760e-02
sample154 -0.0131452472 -8.153903e-04
sample155 -0.0211742574  2.642246e-03
sample156 -0.0117803505  2.698265e-02
sample157 -0.0096167165  1.433840e-02
sample158 -0.0101754772  9.137620e-03
sample159  0.0120662931 -2.565236e-02
sample160 -0.0132238202  2.916023e-03
sample161  0.0274491966 -1.748284e-02
sample162  0.0012482909  3.152261e-02
sample163  0.0042031315  1.830701e-02
sample164  0.0174896157 -1.175915e-02
sample165  0.0097517662 -6.119019e-03
sample166  0.0190134679 -1.121582e-02
sample167 -0.0044140836  4.665585e-03
sample168  0.0049689168 -1.941822e-02
sample169 -0.0209802098  3.498729e-03
> o2plsRes@scores$dist[[2]] ## Distinctive scores for Block 2
                   [,1]          [,2]
sample1   -0.0515543627 -0.0305856787
sample2   -0.0144993256  0.0236342950
sample3   -0.0371833108 -0.0140263348
sample4    0.0068945388 -0.0132539692
sample5    0.0215035333 -0.0663338101
sample6   -0.0187055152  0.0088773016
sample7   -0.0061521552  0.0064029054
sample8   -0.0210874459  0.0334652901
sample9    0.0516865043 -0.0291142799
sample10   0.0059440366 -0.0527217447
sample11   0.0393010793 -0.0200624712
sample12  -0.0420837100  0.0131331362
sample13   0.0333252565  0.0818552509
sample14  -0.0190062644  0.0160202175
sample15  -0.0030968049 -0.0189230681
sample16  -0.0004452158  0.0018880102
sample17  -0.0185848615  0.0240170131
sample18  -0.0273093598  0.0230213640
sample19  -0.0217761111 -0.0445894441
sample20   0.0245820821  0.0159812738
sample21   0.0034527644 -0.0400016054
sample22  -0.0340789054  0.0039289109
sample23  -0.0010344929 -0.0310161212
sample24   0.0289468503  0.0760962436
sample25  -0.0119098496 -0.0122798760
sample26  -0.0181001057  0.0517892852
sample27   0.0050465417 -0.0086515844
sample28   0.0057491502  0.0358830107
sample29  -0.0051104246  0.0116605117
sample30  -0.0103085904  0.0039678538
sample31  -0.0319929858  0.0090606113
sample32  -0.0036232521 -0.0328202010
sample33  -0.0534742153  0.0024751837
sample34  -0.0067495749 -0.0111000311
sample35   0.0378745721  0.0465929296
sample36   0.0647886800  0.0359987924
sample37   0.0488441236  0.0492906912
sample38  -0.0251514062  0.0197110110
sample39  -0.0085428066 -0.0105117852
sample40   0.0379324087  0.0440810741
sample41  -0.0044199152 -0.0128820644
sample42  -0.0292553573 -0.0067045265
sample43  -0.0077829155 -0.0510178219
sample44   0.0045122248  0.0479660309
sample45  -0.0074444298 -0.0051116726
sample46  -0.0088025512  0.0196186661
sample47   0.0076696301  0.0215947965
sample48   0.0290108585 -0.0175568376
sample49  -0.0141754858  0.0184717099
sample50   0.0006282201 -0.0233054373
sample51   0.0441995177 -0.0410022921
sample52   0.0715329391 -0.0399499475
sample53  -0.0095954087 -0.0029140909
sample54   0.0048933768 -0.0281884386
sample55   0.0327325487 -0.0532290012
sample56   0.0323068984 -0.0256595538
sample57   0.0806603122 -0.0286748097
sample58  -0.0064792049 -0.0006945349
sample59   0.0088958941  0.0067389649
sample60   0.0874124612  0.0431964341
sample61   0.0577604571 -0.0326112099
sample62  -0.0313318464  0.0224391756
sample63  -0.0233625220  0.0125110562
sample64  -0.0086426068  0.0148770341
sample65   0.0025256193 -0.0404466327
sample66   0.0006014071 -0.0471576264
sample67   0.0706087042  0.0516228406
sample68   0.0082301011  0.0033109509
sample69  -0.0475076743  0.0001452708
sample70  -0.0600773716  0.0089986962
sample71  -0.0096321627 -0.0050761187
sample72  -0.0031773546 -0.0166221542
sample73  -0.0113700517 -0.0191726684
sample74  -0.0014179662 -0.0608101325
sample75   0.0041911740 -0.0399981269
sample76  -0.0055326449  0.0353114263
sample77  -0.0260214459  0.0305731380
sample78  -0.0119267436  0.0632236007
sample79   0.0186017239  0.0027402910
sample80   0.0241047889 -0.0472697181
sample81  -0.0220288317 -0.0079577210
sample82  -0.0180751258  0.0639051029
sample83  -0.0256671713 -0.0125898269
sample84   0.0161392598 -0.0567222449
sample85   0.0139988188  0.0322763454
sample86  -0.0198382995  0.0389225776
sample87   0.0266270281 -0.0032979996
sample88   0.0515677078  0.0117902495
sample89   0.0014022125 -0.0140510488
sample90  -0.0375949749  0.0044004551
sample91   0.0310397965  0.0440610926
sample92   0.0270570567  0.0324380452
sample93  -0.0215009202  0.0063993941
sample94  -0.0415702912 -0.0037692077
sample95  -0.0168416047  0.0010019120
sample96  -0.0285582661 -0.0187991000
sample97  -0.0490843868 -0.0266760748
sample98  -0.0171579033 -0.0112897471
sample99  -0.0271316525  0.0232395583
sample100 -0.0301789816  0.0305498693
sample101 -0.0264371151  0.0170723968
sample102  0.0012767734 -0.0248949597
sample103  0.0055214687 -0.0030040587
sample104  0.0251346074 -0.0165212671
sample105  0.0062424215 -0.0400309901
sample106  0.0069768684  0.0154982315
sample107 -0.0315912602 -0.0118883820
sample108 -0.0109690679  0.0023637162
sample109 -0.0014762845  0.0165583675
sample110  0.0036971063  0.0168260726
sample111 -0.0071624739 -0.0345651461
sample112  0.0046098120 -0.0048009350
sample113  0.0082236008 -0.0383233357
sample114 -0.0293642209 -0.0165595240
sample115 -0.0003260453  0.0135805368
sample116  0.0183575759  0.0665377581
sample117  0.0227640036 -0.0012287760
sample118  0.0015695248  0.0472617382
sample119  0.0190084932  0.0590034062
sample120 -0.0449645755  0.0072755697
sample121  0.0077307184  0.0104738937
sample122 -0.0027132063 -0.0394983138
sample123  0.0016959300  0.0028593594
sample124 -0.0365091615  0.0040382925
sample125 -0.0053658663 -0.0316029164
sample126 -0.0458032408  0.0019165544
sample127 -0.0494064872  0.0088209044
sample128 -0.0155454766  0.0186819802
sample129 -0.0184340400  0.0038684312
sample130 -0.0303640987 -0.0052225766
sample131 -0.0088697422  0.0156339713
sample132 -0.0433916471 -0.0154075483
sample133  0.0204029276 -0.0282209049
sample134  0.0175513332  0.0262883962
sample135  0.0029009925  0.0017003151
sample136 -0.0367997573 -0.0072249751
sample137 -0.0348600323  0.0075400273
sample138 -0.0044063824 -0.0053752428
sample139  0.0073103935  0.0308956174
sample140  0.0039925654 -0.0167019605
sample141 -0.0184093462 -0.0387953445
sample142  0.0268670676 -0.0239229634
sample143  0.0421049126 -0.0110888235
sample144  0.0017253664 -0.0341766012
sample145  0.0681741320 -0.0073526377
sample146 -0.0239965222  0.0118396767
sample147 -0.0063453522  0.0183130585
sample148  0.0230825251 -0.0379753037
sample149  0.0223298673  0.0188909118
sample150  0.0055709108  0.0174179009
sample151  0.0039177786 -0.0233533275
sample152  0.0134325667  0.0302344591
sample153  0.0511990309  0.0730230140
sample154  0.0006698324  0.0154177486
sample155  0.0032926626 -0.0288651601
sample156 -0.0016463495 -0.0474657733
sample157 -0.0045857599  0.0154934573
sample158  0.0201775524 -0.0332982124
sample159 -0.0086909001  0.0073496711
sample160  0.0295437331 -0.0555734536
sample161  0.0332754288  0.0033779619
sample162  0.0121954537  0.0433540412
sample163 -0.0173490933  0.0227219128
sample164  0.0143374783 -0.0453542590
sample165  0.0343612593 -0.0511194536
sample166 -0.0157536004  0.0094621170
sample167 -0.0179654624 -0.0006982358
sample168 -0.0033829919  0.0060747155
sample169  0.0116231468 -0.0015112800
> 
> ## 3.3 Plotting VAF
> 
> # DISCO-SCA plotVAF
> plotVAF(discoRes)
> 
> # JIVE plotVAF
> plotVAF(jiveRes)
> 
> 
> #########################
> ## PART 4. Plot Results
> 
> # Scores for common part. DISCO-SCA
> plotRes(object=discoRes,comps=c(1,2),what="scores",type="common",
+              combined=FALSE,block=NULL,color="classname",shape=NULL,labels=NULL,
+              background=TRUE,palette=NULL,pointSize=4,labelSize=NULL,
+              axisSize=NULL,titleSize=NULL)
> 
> # Scores for common part. JIVE
> plotRes(object=jiveRes,comps=c(1,2),what="scores",type="common",
+              combined=FALSE,block=NULL,color="classname",shape=NULL,labels=NULL,
+              background=TRUE,palette=NULL,pointSize=4,labelSize=NULL,
+              axisSize=NULL,titleSize=NULL)
> 
> # Scores for common part. O2PLS.
> p1 <- plotRes(object=o2plsRes,comps=c(1,2),what="scores",type="common",
+               combined=FALSE,block="expr",color="classname",shape=NULL,
+               labels=NULL,background=TRUE,palette=NULL,pointSize=4,
+               labelSize=NULL,axisSize=NULL,titleSize=NULL)
> p2 <- plotRes(object=o2plsRes,comps=c(1,2),what="scores",type="common",
+               combined=FALSE,block="mirna",color="classname",shape=NULL,
+               labels=NULL,background=TRUE,palette=NULL,pointSize=4,
+               labelSize=NULL,axisSize=NULL,titleSize=NULL)
> legend <- g_legend(p1)
> grid.arrange(arrangeGrob(p1+theme(legend.position="none"),
+                          p2+theme(legend.position="none"),nrow=1),
+              legend,heights=c(6/7,1/7))
> 
> # Combined plot of scores for common part. O2PLS.
> plotRes(object=o2plsRes,comps=c(1,1),what="scores",type="common",
+              combined=TRUE,block=NULL,color="classname",shape=NULL,
+              labels=NULL,background=TRUE,palette=NULL,pointSize=4,
+              labelSize=NULL,axisSize=NULL,titleSize=NULL)
> 
> 
> # Scores for distinctive part. DISCO-SCA. (two plots one for each block)
> p1 <- plotRes(object=discoRes,comps=c(1,2),what="scores",type="individual",
+               combined=FALSE,block="expr",color="classname",shape=NULL,
+               labels=NULL,background=TRUE,palette=NULL,pointSize=4,
+               labelSize=NULL,axisSize=NULL,titleSize=NULL)
> p2 <- plotRes(object=discoRes,comps=c(1,2),what="scores",type="individual",
+               combined=FALSE,block="mirna",color="classname",shape=NULL,
+               labels=NULL,background=TRUE,palette=NULL,pointSize=4,
+               labelSize=NULL,axisSize=NULL,titleSize=NULL)
> legend <- g_legend(p1)
> grid.arrange(arrangeGrob(p1+theme(legend.position="none"),
+                          p2+theme(legend.position="none"),nrow=1),
+              legend,heights=c(6/7,1/7))
> 
> # Combined plot of scores for distinctive part. DISCO-SCA
> plotRes(object=discoRes,comps=c(1,1),what="scores",type="individual",
+              combined=TRUE,block=NULL,color="classname",shape=NULL,
+              labels=NULL,background=TRUE,palette=NULL,pointSize=4,
+              labelSize=NULL,axisSize=NULL,titleSize=NULL)
> 
> # Combined plot of scores for common and distinctive part. O2PLS (two plots one for each block)
> p1 <- plotRes(object=o2plsRes,comps=c(1,1),what="scores",type="both",
+               combined=FALSE,block="expr",color="classname",shape=NULL,
+               labels=NULL,background=TRUE,palette=NULL,pointSize=4,
+               labelSize=NULL,axisSize=NULL,titleSize=NULL)
> p2 <- plotRes(object=o2plsRes,comps=c(1,1),what="scores",type="both",
+               combined=FALSE,block="mirna",color="classname",shape=NULL,
+               labels=NULL,background=TRUE,palette=NULL,pointSize=4,
+               labelSize=NULL,axisSize=NULL,titleSize=NULL)
> legend <- g_legend(p1)
> grid.arrange(arrangeGrob(p1+theme(legend.position="none"),
+                          p2+theme(legend.position="none"),nrow=1),
+              legend,heights=c(6/7,1/7))
> 
> # Combined plot of scores for common and distinctive part. DISCO  (two plots one for each block)
> p1 <- plotRes(object=discoRes,comps=c(1,1),what="scores",type="both",
+               combined=FALSE,block="expr",color="classname",shape=NULL,
+               labels=NULL,background=TRUE,palette=NULL,pointSize=4,
+               labelSize=NULL,axisSize=NULL,titleSize=NULL)
> p2 <- plotRes(object=discoRes,comps=c(1,1),what="scores",type="both",
+               combined=FALSE,block="mirna",color="classname",shape=NULL,
+               labels=NULL,background=TRUE,palette=NULL,pointSize=4,
+               labelSize=NULL,axisSize=NULL,titleSize=NULL)
> legend <- g_legend(p1)
> grid.arrange(arrangeGrob(p1+theme(legend.position="none"),
+                          p2+theme(legend.position="none"),nrow=1),
+              legend,heights=c(6/7,1/7))
> 
> # Loadings for common part. DISCO-SCA. (two plots one for each block)
> p1 <- plotRes(object=discoRes,comps=c(1,2),what="loadings",type="common",
+               combined=FALSE,block="expr",color="classname",shape=NULL,
+               labels=NULL,background=TRUE,palette=NULL,pointSize=4,
+               labelSize=NULL,axisSize=NULL,titleSize=NULL)
> p2 <- plotRes(object=discoRes,comps=c(1,2),what="loadings",type="common",
+               combined=FALSE,block="mirna",color="classname",shape=NULL,
+               labels=NULL,background=TRUE,palette=NULL,pointSize=4,
+               labelSize=NULL,axisSize=NULL,titleSize=NULL)
> grid.arrange(arrangeGrob(p1+theme(legend.position="none"),
+                          p2+theme(legend.position="none"),nrow=1),
+              heights=c(6/7,1/7))
> 
> 
> # Loadings for distinctive part. DISCO-SCA. (two plots one for each block)
> p1 <- plotRes(object=discoRes,comps=c(1,2),what="loadings",type="individual",
+               combined=FALSE,block="expr",color="classname",shape=NULL,
+               labels=NULL,background=TRUE,palette=NULL,pointSize=4,
+               labelSize=NULL,axisSize=NULL,titleSize=NULL)
> p2 <- plotRes(object=discoRes,comps=c(1,2),what="loadings",type="individual",
+               combined=FALSE,block="mirna",color="classname",shape=NULL,
+               labels=NULL,background=TRUE,palette=NULL,pointSize=4,
+               labelSize=NULL,axisSize=NULL,titleSize=NULL)
> grid.arrange(arrangeGrob(p1+theme(legend.position="none"),
+                          p2+theme(legend.position="none"),nrow=1),
+              heights=c(6/7,1/7))
> 
> 
> # Combined plot for loadings from common and distinctive part  (two plots one for each block)
> p1 <- plotRes(object=discoRes,comps=c(1,1),what="loadings",type="both",
+               combined=FALSE,block="expr",color="classname",shape=NULL,
+               labels=NULL,background=TRUE,palette=NULL,pointSize=4,
+               labelSize=NULL,axisSize=NULL,titleSize=NULL)
> p2 <- plotRes(object=discoRes,comps=c(1,1),what="loadings",type="both",
+               combined=FALSE,block="mirna",color="classname",shape=NULL,
+               labels=NULL,background=TRUE,palette=NULL,pointSize=4,
+               labelSize=NULL,axisSize=NULL,titleSize=NULL)
> grid.arrange(arrangeGrob(p1+theme(legend.position="none"),
+                          p2+theme(legend.position="none"),nrow=1),
+              heights=c(6/7,1/7))
> 
> 
> 
> ## Plot scores and loadings togheter: Common components DISCO-SCA
> p1 <- plotRes(object=discoRes,comps=c(1,2),what="both",type="common",
+         combined=FALSE,block="expr",color="classname",shape=NULL,labels=NULL,
+         background=TRUE,palette=NULL,pointSize=4,labelSize=NULL,
+         axisSize=NULL,titleSize=NULL)
> p2 <- plotRes(object=discoRes,comps=c(1,2),what="both",type="common",
+               combined=FALSE,block="mirna",color="classname",shape=NULL,labels=NULL,
+               background=TRUE,palette=NULL,pointSize=4,labelSize=NULL,
+               axisSize=NULL,titleSize=NULL)
> grid.arrange(arrangeGrob(p1+theme(legend.position="none"),
+                          p2+theme(legend.position="none"),nrow=1),
+              heights=c(6/7,1/7))
> 
> 
> ## Plot scores and loadings togheter:  Common components O2PLS
> p1 <- plotRes(object=o2plsRes,comps=c(1,2),what="both",type="common",
+               combined=FALSE,block="expr",color="classname",shape=NULL,labels=NULL,
+               background=TRUE,palette=NULL,pointSize=4,labelSize=NULL,
+               axisSize=NULL,titleSize=NULL)
> p2 <- plotRes(object=o2plsRes,comps=c(1,2),what="both",type="common",
+               combined=FALSE,block="mirna",color="classname",shape=NULL,labels=NULL,
+               background=TRUE,palette=NULL,pointSize=4,labelSize=NULL,
+               axisSize=NULL,titleSize=NULL)
> grid.arrange(arrangeGrob(p1+theme(legend.position="none"),
+                          p2+theme(legend.position="none"),nrow=1),
+              heights=c(6/7,1/7))
> 
> 
> ## Plot scores and loadings togheter: Distintive components DISCO-SCA
> p1 <- plotRes(object=discoRes,comps=c(1,2),what="both",type="individual",
+               combined=FALSE,block="expr",color="classname",shape=NULL,labels=NULL,
+               background=TRUE,palette=NULL,pointSize=4,labelSize=NULL,
+               axisSize=NULL,titleSize=NULL)
> p2 <- plotRes(object=discoRes,comps=c(1,2),what="both",type="individual",
+               combined=FALSE,block="mirna",color="classname",shape=NULL,labels=NULL,
+               background=TRUE,palette=NULL,pointSize=4,labelSize=NULL,
+               axisSize=NULL,titleSize=NULL)
> grid.arrange(arrangeGrob(p1+theme(legend.position="none"),
+                          p2+theme(legend.position="none"),nrow=1),
+              heights=c(6/7,1/7))
> 
> 
> 
> 
> proc.time()
   user  system elapsed 
 12.947   0.239  13.205