CorrelationMap: Heatmap of correlations between bacterial taxa and host...

In katrikorpela/mare: Microbiota Analysis in R Easily

Heatmap of correlations between bacterial taxa and host variables

Description

Calculates the correlations between bacterial taxa and selected variables in the metadata file, and plots the correlations as a heatmap.

Usage

CorrelationMap(taxonomic.table, meta, variables, select.by = NULL, 
                           selection = NULL,  outlier.cutoff = 3, readcount.cutoff = 0, 
                           min.abundance = 0, min.prevalence = 0, pdf = F, relative = T)

Arguments

taxonomic.table	Name of the taxonomic table. Should be the name of a text file.
meta	Name of the metadata file containing the grouping variable. Should be the name of a text file.
variables	Names or index numbers of continuous variables in the metadata file to be included in the analysis.
readcount.cutoff	Lowest acceptable read count per sample. Samples with fewer reads are ignored.
select.by	Name of a variable in the metadata file by which a subset will be selected for plotting.
select	Determines which value on the selection variable will be selected for plotting.
outlier.cutoff	Highest acceptable standard deviation from the overall mean abundance for a given taxon. Data points exceeding this value will be replaced by the cut-off value to eliminate disproportional effect of outliers on the results.
min.abundance	Minimum acceptable relative abundance of bacterial taxa. Used with min.prevalence to include only taxa with abundance > min.abundance in > min.prevalence samples.
min.prevalence	Minimum acceptable prevalence of taxa (proportion of all samples). Used with min.abundance to include only taxa with abundance > min.abundance in > min.prevalence cases.
pdf	Should the figure be saved as pdf? If yes, specify TRUE.
relative	Use relative abundances? Default is TRUE. FALSE will use data as is.

Author(s)

Katri Korpela

Examples

## Not run: 
#Plot the correlations between genus-level bacterial taxa and the first 15 variables in the metadata file.
#Select only taxa whose relative abundance is >0.1 in >half of all samples.
#Save the plot as PDF.

CorrelationMap(taxonomic.table = 'organised_genus_table.txt',
                meta = 'meta.txt', 
                variables = c(1:15), 
                min.abundance = 0.01,
                min.prevalence = 0.5,
                pdf = T)
	

## End(Not run)

katrikorpela/mare documentation built on July 17, 2022, 2:49 a.m.