phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. See the phyloseq front page:
Hi all- how do I assign the row names in map file to the SampleID sample names? Ive tried a few. different things I've read but nothing has seemed to work.
library(ape)
library(ggplot2)
library(phyloseq)
mothur_data
phyloseq-class experiment-level object
otu_table() OTU Table: [ 4859 taxa and 84 samples ]
tax_table() Taxonomy Table: [ 4859 taxa by 6 taxonomic ranks ]
phy_tree() Phylogenetic Tree: [ 4859 tips and 4858 internal nodes ]
sample_names(mothur_data)
[1] "1.5" "2.1" "2.10" "2.12" "2.2" "2.3" "2.4" "2.5" "2.6" "2.7"
[11] "2.8" "3.1" "3.10" "3.11" "3.12" "3.2" "3.3" "3.4" "3.5" "3.6"
[21] "3.7" "3.8" "4.10" "4.11" "4.12" "4.2" "4.3" "4.4" "4.5" "4.6"
[31] "4.8" "4.9" "5.10" "5.2" "5.3" "5.4" "5.5" "5.6" "5.7" "5.8"
[41] "6.1" "6.10" "6.11" "6.2" "6.3" "6.4" "6.5" "6.6" "6.7" "6.8"
[51] "6.9" "7.1" "7.2" "7.3" "7.4" "7.5" "7.6" "7.7" "7.8" "7.9"
[61] "8.1" "8.10" "8.11" "8.12" "8.2" "8.3" "8.4" "8.5" "8.6" "8.7"
[71] "8.8" "8.9" "9.10" "9.12" "9.13" "9.2" "9.3" "9.4" "9.5" "9.6"
[81] "9.7" "9.8" "9.9" "NTC"
sample_names(mothur_map)
[1] "sa1" "sa2" "sa3" "sa4" "sa5" "sa6" "sa7" "sa8" "sa9" "sa10"
[11] "sa11" "sa12" "sa13" "sa14" "sa15" "sa16" "sa17" "sa18" "sa19" "sa20"
[21] "sa21" "sa22" "sa23" "sa24" "sa25" "sa26" "sa27" "sa28" "sa29" "sa30"
[31] "sa31" "sa32" "sa33" "sa34" "sa35" "sa36" "sa37" "sa38" "sa39" "sa40"
[41] "sa41" "sa42" "sa43" "sa44" "sa45" "sa46" "sa47" "sa48" "sa49" "sa50"
[51] "sa51" "sa52" "sa53" "sa54" "sa55" "sa56" "sa57" "sa58" "sa59" "sa60"
[61] "sa61" "sa62" "sa63" "sa64" "sa65" "sa66" "sa67" "sa68" "sa69" "sa70"
[71] "sa71" "sa72" "sa73" "sa74" "sa75" "sa76" "sa77" "sa78" "sa79" "sa80"
[81] "sa81" "sa82" "sa83" "sa84"
mothur_map
Sample Data: [84 samples by 4 sample variables]:
SampleID Treatment Sex Parasites
sa1 1.5 C U N
sa2 2.1 P U N
sa3 2.2 P U Y
sa4 2.3 P U N
sa5 2.4 P U N
sa6 2.5 P U N
sa7 2.6 P U N
sa8 2.7 P U N
sa9 2.8 P U N
sa10 2.10 P U
Hi all- how do I assign the row names in map file to the SampleID sample names? Ive tried a few. different things I've read but nothing has seemed to work.