[R] Principle Coordinate Analysis of unweighted UniFrac distances on R

[Thilini Maddegoda Vidanelage]

Dear all,

First of all, I am so grateful if you can help me
in analyzing principle coordinate analysis of unweighted UniFrac distances
on R.


I am analyzing microbial species profile of an individual (BA) versus
reference population (HMP) and want to generate a PCoA graph to see whether
there any clusters of OTUs related to my samples.



In a table, I have OTUs (percentages) for 6 replicates of one subject (BA)
and 2910 reference subjects. Below is the format [it has only 9 subjects
(including 6 replicates of one subject and 3 reference subjects) in rows
and 5 microbial species in columns]. The second column shows the type of
sample whether it a BA or HMP.



SampleName

Group

g__Abiotrophia

g__Acetanaerobacterium

g__Acetatifactor

g__Acetivibrio

g__Acetobacter

1970_I

BA

0

0.038857

0.003473

0

0

1970_III

BA

0

0.035763

0

0

0

1970_IV

BA

0

0.021248

0

0

0

2016_I

BA

0

0.015537

0

0

0

2016_II

BA

0

0.02313

0

0

0

2016_III

BA

0

0.021606

0

0

0

X700110831

HMP

0

0

0

0

0

X700021898

HMP

0

0

0

0

0

X700113546

HMP

0

0

0

0

0



I have been trying to generate the graph for 5-6 days by looking at
different tutorials but  I am not succeeded in generating the graph that I
wanted yet. After doing some tutorials, I installed these packages such as
Ggplot2, dplyr, dendextend, RColorBrewer, vegan, GUniFrac, labdsv in R.

Is there anyone who can guide me in this or suggest a tutorial which helps
me to do the analysis step by step. I am a newbie to R.

Any help is much more appreciated.



Many thanks and best regards,
*Thilini Jayasinghe*
PhD Candidate
Liggins Institute
The University of Auckland
Building 503/201, 85 Park Road, Grafton, Auckland 2023
Mobile: +64 220211604
Email: tmad109 at aucklanduni.ac.nz

	[[alternative HTML version deleted]]