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Principle Coordinate Analysis of unweighted UniFrac distances on R

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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: [hidden email]

        [[alternative HTML version deleted]]

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
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Re: Principle Coordinate Analysis of unweighted UniFrac distances on R

Bert Gunter-2
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
<[hidden email]> 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: [hidden email]
>
>         [[alternative HTML version deleted]]
>
> ______________________________________________
> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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Re: Principal Coordinate Analysis of unweighted UniFrac distances on R

Martin Maechler
>>>>> Bert Gunter <[hidden email]>
>>>>>     on Mon, 13 Mar 2017 10:39:49 -0700 writes:

    > 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

    [....]

and *PLEASE* do spell it correctly : "principal",  *NOT* 'principle'
(I've corrected it in the 'Subject' as I don't want to create another
 google hit for the wrong spelling ...)

Martin Maechler

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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