Description Usage Arguments Details Author(s) References Examples
Calcualte the top taxa relative abundance normalized to the overall bacterial load. Prepare the data frame for graphing.
1 2 3 4 5 6 7 | topAbsAbundDataFrame(rel.abund,
bac.load,
bac.load.id="bac_load",
abund.id.col="Abundance",
subject.id.col="SubjectID",
tmpt.id.col="Time_point",
bacteria.id.col="Bacteria")
|
rel.abund |
The transposed relative abundance |
bac.load |
The |
bac.load.id |
Name of the bacterial load value column. Default is "bac_load". |
abund.id.col |
Name of the column containing the relative abundance values for the top taxa relative abundance. Default is "Abundance". |
subject.id.col |
Name of the subject ID column. Default is "SubjectID". |
tmpt.id.col |
Name of the time point column. Default is "Time_point". |
bacteria.id.col |
Name of the column to contain the bacterial load values. Default is "Bacteria". |
Package: | patPRO |
Type: | Package |
Version: | 1.0.0 |
Date: | 2015-09-18 |
License: | GPLv3 |
An overview of how to use the package, including the most important functions, is included in the supplemental R notebook patPROExampleWorkflow.html.
Geoffrey Hannigan <ghanni@upenn.edu>, Loesche MA, Hodkinson BP, Mehta S, Elizabeth Grice <egrice@upenn.edu>
patPRO: An R package for the visualization of longitudinal microbiome data. Hannigan GD, Loesche MA, Hodkinson BP, Mehta S, Grice EA.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 | data("PatProOTU",package="patPRO")
data("PatProMap",package="patPRO")
data("PatProBacLoad",package="patPRO")
transTestRelAbund <- transposeRelAbund(PatProOTU)
mergedMapTransRA <- mergeMapMetaData(map.file=PatProMap,
merging.file=transTestRelAbund,
map.sub.id="SubjectID",
map.tmpt="Time_point",
map.smpl.id="SampleID",
sample.id.col="SampleID")
top5RelAbund <- topRelAbundDataFrame(x=mergedMapTransRA, top.taxa.num=5)
mergedMapBacLoad <- mergeMapMetaData(map.file=PatProMap,
merging.file=PatProBacLoad,
map.sub.id="SubjectID",
map.tmpt="Time_point",
map.smpl.id="SampleID",
sample.id.col="SampleID")
absAbundOutDf <- topAbsAbundDataFrame(top5RelAbund, mergedMapBacLoad, bac.load.id="Num_Bacteria")
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