OTU.recap: Summarize OTU

In RAM: R for Amplicon-Sequencing-Based Microbial-Ecology

Description

This function summarize OTU table at each given taxonomic ranks.

Usage

OTU.recap(data, ranks=c("p", "c", "o", "f", "g"),
          brewer.pal="Pastel1", file=NULL, ext="pdf",
          width=12, height=8)

Arguments

data	a list of otu tables. See also RAM.input.formatting.
ranks	a vector of taxonomic ranks. See also RAM.rank.formatting
brewer.pal	one of the color patterns available in RColorBrewer. See brewer.pal for available selections.
file	filename to save the plot.
ext	extention of the filename to save the plot.
width	width of the plot
height	heigth of the plot

Value

This function returns either a data frame or a list of data frames. If a single otu was provided, it returns the a dataframe with information of how many otuIDs and sequences being classified at selected taxonomic ranks. If more than 1 otu tables being provided, it returns a list, with the first a few are data frames of classification summary of each otu table, the last is a list showing taxa found only in one of the otu data set. This function also generates a barplot for the percent classified otus and sequences at each given rank.

Note

warning is raised when run strsplit() and can be ignored.

Author(s)

Wen Chen

See Also

RAM.rank.formatting and RAM.input.formatting.

Examples

data(ITS1, ITS2)
ranks <- c("p", "c", "o", "f", "g")
df <- OTU.recap(data=list(ITS1=ITS1, ITS2=ITS2), ranks=ranks)
class(df)

Example output

Loading required package: vegan
Loading required package: permute
Loading required package: lattice
This is vegan 2.5-4
Loading required package: ggplot2
Using ind as id variables
Using ind as id variables
Warning message:
In brewer.pal(len, brewer.pal) :
  n too large, allowed maximum for palette Pastel1 is 9
Returning the palette you asked for with that many colors

[1] "list"

RAM documentation built on May 2, 2019, 3:04 p.m.