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: tmad...@aucklanduni.ac.nz
[[alternative HTML version deleted]]
______________________________________________
R-help@r-project.org 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.
