RAM (version 1.2.0)

OTU.recap: Summarize OTU

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.

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)