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

[Bert Gunter]

Please read and follow the posting guide.

Plain text only + code that you tried + reproducible exam (google it).

In general, we do not do tutorials here, but someone may indeed be
able to refer you to one on the web. Googling "principal coordinates
analysis tutorial R" appeared to bring up relevant hits, including a
tutorial using the vegan package functionality.

Cheers,
Bert
Bert Gunter

"The trouble with having an open mind is that people keep coming along
and sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )


On Sun, Mar 12, 2017 at 10:52 PM, Thilini Maddegoda Vidanelage
<tmad109 at aucklanduni.ac.nz> wrote:
> 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]]
>
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