quickChemoDiv {chemodiv} | R Documentation |
Quickly calculate or plot chemodiversity
Description
This function is a shortcut that makes use of many of the other functions in the package. In one simple step chemodiversity is calculated, and if requested also plotted, for users wanting to quickly explore their data using standard parameters.
Usage
quickChemoDiv(
sampleData,
compoundData = NULL,
groupData = NULL,
outputType = "plots"
)
Arguments
sampleData |
Data frame with the relative concentration of each compound (column) in every sample (row). |
compoundData |
Data frame with the compounds in |
groupData |
Grouping data (e.g. population, species etc.). Should be either a vector, or a data frame with a single column. |
outputType |
Type of output that should be returned: either
|
Details
The function requires sample data as input, and can also include
compound data. chemoDivCheck
can be used to ensure these
datasets are correctly formatted, see chemodiv
for further
details on data formatting. If only sample data is supplied,
phytochemical diversity and dissimilarity will be calculated
as Hill diversity and Bray-Curtis dissimilarity, respectively.
If sample data and compound data is supplied, phytochemical diversity
and dissimilarity will be calculated as Functional Hill diversity
and Generalized UniFrac dissimilarity, respectively.
This function then uses the following other functions in the package:
-
compDis
is used to calculate compound dissimilarities using PubChem Fingerprints, if compound data is supplied. -
calcDiv
is used to calculate (Functional) Hill Diversity for q = 1. -
calcDivProf
is used to calculate a diversity profile with (Functional) Hill Diversity for q = 0-3. -
sampDis
is used to calculate Bray-Curtis or Generalized UniFrac dissimilarities between samples. -
chemoDivPlot
is used to create different chemodiversity plots if requested.
quickChemoDiv
is designed to provide an easy way to calculate and
visualize the most central measures of phytochemical diversity. It uses
default parameters to do so, which should be reasonable in most cases.
However, for detailed analyses it is recommended to use the separate
functions to allow for full control of function input, arguments and output.
Value
Different types of chemodiversity measures, either as elements in
a list or as separate plots. If outputType = "data"
, function returns
a compound dissimilarity matrix (if compound data was supplied),
a data frame with (Functional) Hill Diversity at q = 1,
a data frame with a (Functional) Hill Diversity profile for q = 0-3,
and a sample dissimilarity matrix. If outputType = "plots"
,
these data sets are plotted as a dendrogram (if compound data was supplied),
a boxplot, a diversity profile plot and an NMDS plot, respectively.
Examples
data(minimalCompData)
data(minimalSampData)
groups <- c("A", "A", "B", "B")
quickChemoDiv(sampleData = minimalSampData, groupData = groups,
outputType = "data") # Without compound data
data(alpinaSampData)
data(alpinaPopData)
quickChemoDiv(sampleData = alpinaSampData, outputType = "plots",
groupData = alpinaPopData) # Without compound data