Description Usage Arguments Details Author(s) References Examples
Uses the results from the top.rel.abund.data.frame function for graphing relative abundance of the top taxonomy.
1 2 3 4 5 6 7 8 9 10 11 | plotTopTaxa(top.taxa.data.frame,
pat.id,
subject.id.col="SubjectID",
tmpt.id.col="Time_point",
y.lab="Percent Relative Abundance",
x.lab="Time Point", plot.title,
mark.events=FALSE, mark.times,
mark.text="",
color.brewer.set="",
color.manual.set="",
legend.text.size = 7)
|
top.taxa.data.frame |
The |
pat.id |
The patient identifier to specify the case which should be visualized. |
subject.id.col |
Name of the subject ID column found in x. Default is "SubjectID". |
tmpt.id.col |
Name of the time point column found in x. Default is "Time_point". |
y.lab |
Name of the y axis label to be used in the plot. Default is "Percent Relative Abundance". |
x.lab |
Name of the x axis label to be used in the plot. Default is "Time Point". |
plot.title |
The desired plot title. |
mark.events |
Specify whether arrows will be used to specify specific time events. Set as TRUE for using arrows. Default is FALSE. |
mark.times |
The time points to be marked with arrows when mark.events=TRUE. These numbers need to be set as a vector. |
mark.text |
The text to be used to annotate the arrow markers when mark.events=TRUE. |
color.brewer.set |
Name of the color brewer palet to use for plot coloring. Default value uses default colors. |
color.manual.set |
Name of the manually specified color palet to use for plot coloring. Default value uses default colors. |
legend.text.size |
Allows the user to manually set the figure legend text size digit. Default is size 7. |
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")
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)
topTaxa <- plotTopTaxa(top5RelAbund,
1,
plot.title="Subject One Taxonomy",
color.brewer.set="Set2",
mark.events=TRUE,
mark.times=c(2,6),
mark.text="Surgery",
legend.text.size=8)
|
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