plot_ordiplot_core: Plotting core microibota on ordinations

In microsud/microbiomeutilities-shiny: microbiomeutilities: An R package with utility functions for the microbiome R package

Description

This function will plot the ordaination alsong with highligthing the core microbes on the species ordination.

Usage

plot_ordiplot_core(x, ordiObject, coreplot = c(TRUE, FALSE), prevalences,
  detections, color.opt, shape)

Arguments

x	phyloseq-class object
ordiObject	Output of ordinate from package phyloseq. Only NMDS and Bray supported.
coreplot	TRUE or FALSE for core heatmap from microbiome package.
prevalences	Prevalences as supported by microbiome package.
detections	Detections as supported by microbiome package.
color.opt	Variable of interest from metadata.
shape	Variable of interest from metadata.

Details

Most commonly it is observed that the taxonomy file has classification until a given taxonomic level. Hence, to avoid loss of OTU information while using the function tax_glom() for merging at a specific taxonomic level. we will fill the empty cells with the maximum classification available along with the OTU number. This code is a slight modification. the code from ampvis phyloseq-class. Here, we directly take the phyloseq object as input and make the necessary formatting.

Value

plot

Examples

## Not run: 
  # Example data
    library(microbiome)
    library(microbiomeUtilities)
    library(RColorBrewer)
    data("biogeogut")
    p0 <- biogeogut
    ps1 <- format_phyloseq(ps0)
    px <- plot_ordiplot_core(ps1, ordiObject = ordi, coreplot = TRUE, 
    prevalences = prev.thres,
    detections = det.thres, color.opt = "SampleType", shape = NULL)
          
## End(Not run)

microsud/microbiomeutilities-shiny documentation built on May 7, 2019, 9:38 a.m.