Description Usage Arguments Value Author(s) Examples
creates a Sample-by-OT table, filters the table by abundance too if needed, and optionally plots the results.
1 | SampleXOT_Table(OT.seq.concat = OT.seq.concat, ENV = ENV, mosaicPlot = TRUE, filterByMinAbund = 0)
|
OT.seq.concat |
vector or a matrix of sequence ids (rows) by oligotypes, as produced by MED(). |
ENV |
vector of characters. the sample identification for each sequence. typically produced by using GetEnvironmentDatafromFileR(File,Start=2,Stop=15,test=FALSE). |
mosaicPlot |
logical. Whether a mosaic plot is to be plotted. |
filterByMinAbund |
numeric. Whether the final abundance table is to be filtered by minimum abundance of each OT (column sum should be >= filterByMinAbund). 0 indicates no filtering. |
Returns a list with one element if filterByMinAbund=0, and with two elements if filterByMinAbund>0. The first element is the unfiltered table, the second element the filtered table.
Alban Ramette
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 | #File="mock-env-aligned.fasta"
OT.seq.concat <- MED(File,minseq=21,entropymin=0.6,Plot=FALSE)
ENV <- GetEnvironmentDatafromFileR(File,Start=2,Stop=15,test=FALSE)
Table <- SampleXOT_Table(OT.seq.concat=OT.seq.concat,
ENV=ENV,
mosaicPlot=TRUE,
filterByMinAbund= 10
)
Table
#$SamplexOT.table
# Oligotypes
#Samples A C T
# Environment-01 0 24 226
# Environment-02 1 24 225
# Environment-03 0 24 226
# Environment-04 2 25 223
# Environment-05 0 23 227
# Environment-06 0 227 23
# Environment-07 0 227 23
# Environment-08 1 226 23
# Environment-09 0 227 23
# Environment-10 0 226 24
#
#$SamplexOT.table.filtered
# Oligotypes
#Samples C T
# Environment-01 24 226
# Environment-02 24 225
# Environment-03 24 226
# Environment-04 25 223
# Environment-05 23 227
# Environment-06 227 23
# Environment-07 227 23
# Environment-08 226 23
# Environment-09 227 23
# Environment-10 226 24
|
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