| topRelAbundDataFrame {patPRO} | R Documentation |
Prepare the data frame for graphing of the relative abundances of the defined top taxa using the transposed output (originally from Qiime) using 'transposeRelAbund'.
topRelAbundDataFrame(x, top.taxa.num, subject.id.col="SubjectID", sample.id.col="SampleID", tmpt.id.col="Time_point")
x |
The transposed relative abundance |
top.taxa.num |
The number of top taxa requested. |
subject.id.col |
Name of the subject ID column found in x. Default is "SubjectID". |
sample.id.col |
Name of the sample ID column found in x. Default is "SampleID". |
tmpt.id.col |
Name of the time point column found in x. Default is "Time_point". |
| 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.
data("PatProOTU",package="patPRO")
data("PatProMap",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")
top5_rel_abund <- topRelAbundDataFrame(x=mergedMapTransRA, top.taxa.num=5)