inflPlot: A ggplot line plot showing the influences

In combi: Compositional omics model based visual integration

Description

A ggplot line plot showing the influences

Usage

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)), ...)

Arguments

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

Details

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

Value

A ggplot object

Examples

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)

combi documentation built on Nov. 8, 2020, 5:34 p.m.