Nothing
## ----load-packages, warning=FALSE, message=FALSE, echo=FALSE------------------
knitr::opts_chunk$set(cache = FALSE, 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("extdata", "zhangFits.RData", package = "combi"))
## ----install, eval = FALSE----------------------------------------------------
# library(BiocManager)
# BiocManager::install("combi", update = FALSE)
## ----installDevtools, eval = FALSE--------------------------------------------
# library(devtools)
# install_github("CenterForStatistics-UGent/combi")
## ----loadcombipackage---------------------------------------------------------
suppressPackageStartupMessages(library(combi))
cat("combi package version",
as.character(packageVersion("combi")), "\n")
## ----loadData-----------------------------------------------------------------
data(Zhang)
## ----unconstr-----------------------------------------------------------------
microMetaboInt = combi(
list("microbiome" = zhangMicrobio, "metabolomics" = zhangMetabo),
distributions = c("quasi", "gaussian"), compositional = c(TRUE, FALSE),
logTransformGaussian = FALSE)
## ----show---------------------------------------------------------------------
microMetaboInt
## ----simplePlot---------------------------------------------------------------
plot(microMetaboInt)
## ----colourPlot---------------------------------------------------------------
plot(microMetaboInt, samDf = zhangMetavars, samCol = "ABX")
## ----cloudPlot----------------------------------------------------------------
plot(microMetaboInt, samDf = zhangMetavars, samCol = "ABX",
featurePlot = "points")
## ----denPlot------------------------------------------------------------------
plot(microMetaboInt, samDf = zhangMetavars, samCol = "ABX",
featurePlot = "density")
## ----projections--------------------------------------------------------------
#First define the plot, and return the coordinates
mmPlot = plot(microMetaboInt, samDf = zhangMetavars, samCol = "ABX", returnCoords = TRUE, featNum = 10)
#Providing feature names, and sample coordinates, but any combination is allowed
addLink(mmPlot, links = cbind("Staphylococcus_819c11","OTU929ffc"), Views = 1, samples = c(0,1))
## ----extractCoords------------------------------------------------------------
coords = extractCoords(microMetaboInt, Dim = c(1,2))
## ----constr-------------------------------------------------------------------
microMetaboIntConstr = combi(
list("microbiome" = zhangMicrobio, "metabolomics" = zhangMetabo),
distributions = c("quasi", "gaussian"), compositional = c(TRUE, FALSE),
logTransformGaussian = FALSE, covariates = zhangMetavars)
## ----printConstr--------------------------------------------------------------
microMetaboIntConstr
## ----colourPlotConstr---------------------------------------------------------
plot(microMetaboIntConstr, samDf = zhangMetavars, samCol = "ABX")
## ----convPlot-----------------------------------------------------------------
convPlot(microMetaboInt)
## ----inflPlot-----------------------------------------------------------------
inflPlot(microMetaboInt, samples = 1:20, plotType = "boxplot")
## ----sessionInfo--------------------------------------------------------------
sessionInfo()
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