inflPlot {combi} | R Documentation |
A ggplot line plot showing the influences
inflPlot(modelObj, plotType = ifelse(length(modelObj$data) <= 2, "pointplot", "boxplot"), pointFun = "sum", lineSize = 0.07, Dim = 1, samples = seq_len(nrow(if (is.null(modelObj$covariates)) modelObj$latentVars else modelObj$alphas)), ...)
modelObj |
The fitted data integration |
plotType |
The type of plot requested, see details |
pointFun |
The function to calculate the summary measure to be plotted |
lineSize |
The line size |
Dim |
The dimension required |
samples |
index vector of which samples to be plotted |
... |
additional arguments passed on to the influence() function |
The options for plotType are: "pointPlot": Dot plot of total influence per view and sample, "boxplot": plot boxplot of influence of all observations per view and sample, "boxplotSingle": boxplot of log absolute total influence per view, "lineplot": line plot of total influence per view and sample. In the pointplot, dots crosses represent parameter estimates
A ggplot object
data(Zhang) #Unconstrained microMetaboInt = combi( list("microbiome" = zhangMicrobio, "metabolomics" = zhangMetabo), distributions = c("quasi", "gaussian"), compositional = c(TRUE, FALSE), logTransformGaussian = FALSE, verbose = TRUE) #Constrained microMetaboIntConstr = combi( list("microbiome" = zhangMicrobio, "metabolomics" = zhangMetabo), distributions = c("quasi", "gaussian"), compositional = c(TRUE, FALSE), logTransformGaussian = FALSE, covariates = zhangMetavars, verbose = TRUE) load(system.file("extdata", "zhangFits.RData", package = "combi")) inflPlot(microMetaboInt) #Constrained inflPlot(microMetaboIntConstr)