## ----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")) ## ----install, eval = FALSE---------------------------------------------------- # library(BiocManager) # install("RCM", update = FALSE) ## ----loadRCMpackage----------------------------------------------------------- suppressPackageStartupMessages(library(RCM)) cat("RCM package version", as.character(packageVersion("RCM")), "\n") ## ----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"), inflVar = "Age") ## ----inflAgeCol--------------------------------------------------------------- plot(ZellerRCM2constr, plotType = c("variables", "samples"), samColour = "Age") ## ----inflAgeFast2------------------------------------------------------------- plot(ZellerRCM2constr, plotType = c("variables", "samples"), inflVar = "Age", Influence = TRUE, inflDim = 2) ## ----inflDiag----------------------------------------------------------------- plot(ZellerRCM2constr, plotType = c("variables", "samples"), inflVar = "DiagnosisNormal", samShape ="Diagnosis" ) ## ----inflPsi------------------------------------------------------------------ plot(ZellerRCM2, plotType = "samples", samSize = 2.5, inflVar = "psi") ## ----inflPsiConstr------------------------------------------------------------ plot(ZellerRCM2constr, plotType = "samples", samSize = 2.5, inflVar = "psi") ## ----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") ## ----extractCoord------------------------------------------------------------- zellerCoords = extractCoord(ZellerRCM2) str(zellerCoords) ## ----taxaStrongestSignal------------------------------------------------------ taxaSignals = rowSums(zellerCoords$species[, c("end1","end2")]^2) sortedTaxa = taxa_names(ZellerRCM2$physeq)[order(taxaSignals, decreasing = TRUE)] sortedTaxa[1:10] ## ----NonsquaredPlots---------------------------------------------------------- plot(ZellerRCM2, axesFixed = FALSE) ## ----linFewVars, eval = FALSE------------------------------------------------- # #Linear with only 2 variables # ZellerRCM3constr = RCM(Zeller, k = 2, round = TRUE, # covariates = c("Gender","Diagnosis"), responseFun = "linear") ## ----plotFewVars-------------------------------------------------------------- plot(ZellerRCM3constr, plotType = "samples", samColour = "Diagnosis", samShape = "Country") ## ----sessionInfo-------------------------------------------------------------- sessionInfo()