## ----loadRCMpackage------------------------------------------------------
# library(BiocManager)
# BiocManager::install("RCM")
library(RCM)
cat("RCM package version", as.character(packageVersion("RCM")), "\n")

## ----load-packages, warning=FALSE, message=FALSE, echo=FALSE-------------
knitr::opts_chunk$set(cache = TRUE, autodep = TRUE,
                      warning=FALSE, message=FALSE, echo=TRUE, eval=TRUE, 
                      tidy = TRUE, fig.width = 9, fig.height = 6, purl=TRUE, 
                      fig.show = "hold", cache.lazy = FALSE)
palStore = palette()
#Load all fits, to avoid refitting every time rebuilding the vignette
load(system.file("fits", "zellerFits.RData", package = "RCM"))

## ----loadZellerData------------------------------------------------------
data(Zeller)
library(phyloseq)

## ----fitUnconstrainedRCM, eval = FALSE-----------------------------------
#  ZellerRCM2 = RCM(Zeller, k=2, round = TRUE)

## ----ThreeDimensions, eval = FALSE---------------------------------------
#  ZellerRCM3 = RCM(Zeller, k = 3, round = TRUE)

## ----condition, eval = FALSE---------------------------------------------
#  ZellerRCM2cond = RCM(Zeller, k = 2, round = TRUE, confounders = c("Country"))

## ----plotUnconstrainedRCMsam---------------------------------------------
plot(ZellerRCM2, plotType = "samples")

## ----plotUnconstrainedRCMsamCol------------------------------------------
plot(ZellerRCM2, plotType = "samples", samColour = "Diagnosis")

## ----plotUnconstrainedRCMsamColShannon-----------------------------------
plot(ZellerRCM2, plotType = "samples", samColour = "Shannon")

## ----plotUnconstrainedRCMspec--------------------------------------------
plot(ZellerRCM2, plotType = "species")

## ----plotUnconstrainedRCMspec2-------------------------------------------
plot(ZellerRCM2, plotType = "species", taxRegExp = "Fusobacter", 
     taxLabels = TRUE)

## ----plotUnconstrainedRCMspec3-------------------------------------------
plot(ZellerRCM2, plotType = "species", taxLabels = TRUE, taxCol = "Order")

## ----plotUnconstrainedRCMall---------------------------------------------
plot(ZellerRCM2, taxNum = 10, samColour = "Diagnosis")

## ----plotUnconstrainedRCMhighlight---------------------------------------
tmpPlot = plot(ZellerRCM2, taxNum = 10, samColour = "Diagnosis",
               returnCoords = TRUE)
addOrthProjection(tmpPlot, species = "Alloprevotella tannerae",
                  sample = c(-1.2,1.5))

## ----plotAddedDimension--------------------------------------------------
plot(ZellerRCM3, Dim = c(1,3), samColour = "Diagnosis", taxNum = 6)

## ----plotUnconstrainedRCMsamColDev---------------------------------------
plot(ZellerRCM2, plotType = "samples", samColour = "Deviance", samSize = 2.5)

## ----plotUnconstrainedRCMtaxDev------------------------------------------
plot(ZellerRCM3, plotType = "species", taxCol = "Deviance", samSize = 2.5,
     Dim = c(1,2), arrowSize = 0.5)

## ----constrLinAndNP, eval = FALSE----------------------------------------
#  #Linear
#  ZellerRCM2constr = RCM(Zeller, k = 2, round = TRUE,
#                         covariates = c("Age", "Gender","BMI","Country",
#                                        "Diagnosis"), responseFun = "linear")
#  #Nonparametric
#  ZellerRCM2constrNonParam = RCM(Zeller, round = TRUE, k = 2,
#                                 covariates = c("Age","Gender","BMI","Country",
#                                                "Diagnosis"),
#                                 responseFun = "nonparametric")

## ----constrLinPlot-------------------------------------------------------
plot(ZellerRCM2constr, plotType = c("samples"))

## ----constrLinPlot2------------------------------------------------------
plot(ZellerRCM2constr, plotType = c("samples"), samColour = "Diagnosis", 
     samShape = "Country")

## ----plotLinVar----------------------------------------------------------
plot(ZellerRCM2constr, plotType = "variables")

## ----plotnonParamVar-----------------------------------------------------
plot(ZellerRCM2constrNonParam, plotType = "variables")

## ----plotlin2cor---------------------------------------------------------
plot(ZellerRCM2constr, plotType = c("species", "samples"))

## ----plotlin2corVis------------------------------------------------------
tmpPlot2 = plot(ZellerRCM2constr, plotType = c("species", "samples"), 
                returnCoords = TRUE)
addOrthProjection(tmpPlot2, species = "Pseudomonas fluorescens", 
                  sample = c(-12,7))

## ----plotlin3------------------------------------------------------------
plot(ZellerRCM2constr, plotType = c("species", "variables"))

## ----plotlin3Vis---------------------------------------------------------
tmpPlot3 = plot(ZellerRCM2constr, plotType = c("species", "variables"), 
                returnCoords = TRUE)
addOrthProjection(tmpPlot3, species = "Pseudomonas fluorescens", 
                  variable = "DiagnosisSmall_adenoma")

## ----plotlin3Triplot-----------------------------------------------------
plot(ZellerRCM2constr)

## ----plotNPTriplot-------------------------------------------------------
plotRespFun(ZellerRCM2constrNonParam, taxa = NULL ,subdivisions = 50L,
            yLocVar = c(-30, -50,-75,-62.5,-30,-62.5,-70,-50,-30)*0.225, 
            Palette = "Set1", angle = 90, yLocSam = -20,  axisTitleSize = 16, 
            axisLabSize = 11, legendTitleSize = 18, legendLabSize = 12, 
            samShape = "Diagnosis", labSize = 5)

## ----plotnonParamRespFunFuso---------------------------------------------
FusoSpecies = grep("Fusobacterium",value = TRUE,
                   taxa_names(ZellerRCM2constrNonParam$physeq))
plotRespFun(ZellerRCM2constrNonParam, Dim = 1, taxa = FusoSpecies, 
            samShape = "Diagnosis")

## ----plotDevResp---------------------------------------------------------
residualPlot(ZellerRCM2constr, whichTaxa = "response", numTaxa = 6)

## ----plotPearResp--------------------------------------------------------
residualPlot(ZellerRCM2constr, whichTaxa = "response",
             resid = "Pearson", numTaxa = 6)

## ----plotDevRuns---------------------------------------------------------
residualPlot(ZellerRCM2constr, whichTaxa = "runs", resid = "Deviance", 
             numTaxa = 6)

## ----inflAge-------------------------------------------------------------
plot(ZellerRCM2constr, plotType = c("variables", "samples"), Influence = TRUE,
     samColour = "Age" )

## ----inflAgeCol----------------------------------------------------------
plot(ZellerRCM2constr, plotType = c("variables", "samples"), samColour = "Age")

## ----inflAgeFast2--------------------------------------------------------
plot(ZellerRCM2constr, plotType = c("variables", "samples"), samColour = "Age",
     Influence = TRUE, inflDim = 2)

## ----plotUnconstrainedRCMpsis, fig.height = 8, fig.width = 9-------------
plot(ZellerRCM2cond, plotPsi = "psi")

## ----plotUnconstrainedRCMlogliks, fig.height = 8, fig.width = 9----------
plot(ZellerRCM2cond, plotPsi = "loglik")

## ----plotUnconstrainedRCMinertia, fig.height = 8, fig.width = 9----------
plot(ZellerRCM2cond, plotPsi = "inertia")

## ----sessionInfo---------------------------------------------------------
sessionInfo()