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Guillaume Perréal
easy16S
Commits
f5aec7b4
Commit
f5aec7b4
authored
Jan 14, 2019
by
Midoux Cedric
Committed by
Guillaume Perréal
Jan 14, 2019
Browse files
demo : chaillou only
parent
7a514800
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2
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demo/demo.RData
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f5aec7b4
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demo/make-demo.R
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f5aec7b4
library
(
phyloseq
)
library
(
phyloseq
)
data
(
"GlobalPatterns"
)
data
(
"GlobalPatterns"
)
food
<-
food
<-
import_biom
(
import_biom
(
BIOMfilename
=
"chaillou.biom"
,
BIOMfilename
=
"chaillou.biom"
,
treefilename
=
"chaillou.nwk"
,
treefilename
=
"chaillou.nwk"
,
parseFunction
=
parse_taxonomy_greengenes
parseFunction
=
parse_taxonomy_greengenes
)
)
sample_data
(
food
)
<-
sample_data
(
food
)
<-
read.table
(
"chaillou.tsv"
,
read.table
(
"chaillou.tsv"
,
header
=
TRUE
,
header
=
TRUE
,
row.names
=
1
,
row.names
=
1
,
sep
=
"\t"
)
sep
=
"\t"
)
kinetic
<-
kinetic
<-
import_biom
(
BIOMfilename
=
"mach.biom"
,
treefilename
=
"mach.nwk"
)
import_biom
(
BIOMfilename
=
"mach.biom"
,
treefilename
=
"mach.nwk"
)
sample_data
(
kinetic
)
<-
sample_data
(
kinetic
)
<-
read.table
(
"mach.tsv"
,
read.table
(
"mach.tsv"
,
header
=
TRUE
,
header
=
TRUE
,
row.names
=
1
,
row.names
=
1
,
sep
=
"\t"
)
sep
=
"\t"
)
colnames
(
tax_table
(
kinetic
))
<-
c
(
"Kingdom"
,
"Phylum"
,
"Class"
,
"Order"
,
"Family"
,
"Genus"
)
colnames
(
tax_table
(
kinetic
))
<-
c
(
"Kingdom"
,
"Phylum"
,
"Class"
,
"Order"
,
"Family"
,
"Genus"
)
tax_table
(
kinetic
)[
grep
(
"unknown "
,
tax_table
(
kinetic
))]
<-
NA
tax_table
(
kinetic
)[
grep
(
"unknown "
,
tax_table
(
kinetic
))]
<-
NA
ravel
<-
ravel
<-
import_biom
(
BIOMfilename
=
"ravel.biom"
)
import_biom
(
BIOMfilename
=
"ravel.biom"
)
sample_data
(
ravel
)
<-
sample_data
(
ravel
)
<-
read.table
(
"ravel.tsv"
,
read.table
(
"ravel.tsv"
,
header
=
TRUE
,
header
=
TRUE
,
row.names
=
1
,
row.names
=
1
,
sep
=
"\t"
)
sep
=
"\t"
)
colnames
(
tax_table
(
ravel
))
<-
c
(
"Kingdom"
,
"Phylum"
,
"Class"
,
"Order"
,
"Family"
,
"Genus"
,
"Species"
)
colnames
(
tax_table
(
ravel
))
<-
c
(
"Kingdom"
,
"Phylum"
,
"Class"
,
"Order"
,
"Family"
,
"Genus"
,
"Species"
)
tax_table
(
ravel
)[
grep
(
"unknown "
,
tax_table
(
ravel
))]
<-
NA
tax_table
(
ravel
)[
grep
(
"unknown "
,
tax_table
(
ravel
))]
<-
NA
soil
<-
soil
<-
import_biom
(
BIOMfilename
=
"morton.biom"
,
treefilename
=
"morton.tree"
)
import_biom
(
BIOMfilename
=
"morton.biom"
,
treefilename
=
"morton.tree"
)
sample_data
(
soil
)
<-
sample_data
(
soil
)
<-
read.table
(
"morton.csv"
,
read.table
(
"morton.csv"
,
header
=
TRUE
,
header
=
TRUE
,
row.names
=
1
,
row.names
=
1
,
sep
=
"\t"
)
sep
=
"\t"
)
colnames
(
tax_table
(
soil
))
<-
c
(
"Kingdom"
,
"Phylum"
,
"Class"
,
"Order"
,
"Family"
,
"Genus"
,
"Species"
)
colnames
(
tax_table
(
soil
))
<-
c
(
"Kingdom"
,
"Phylum"
,
"Class"
,
"Order"
,
"Family"
,
"Genus"
,
"Species"
)
tax_table
(
soil
)[
grep
(
"unknown "
,
tax_table
(
soil
))]
<-
NA
tax_table
(
soil
)[
grep
(
"unknown "
,
tax_table
(
soil
))]
<-
NA
biorare
<-
biorare
<-
import_biom
(
BIOMfilename
=
"biorare.biom"
,
treefilename
=
"biorare.nwk"
)
import_biom
(
BIOMfilename
=
"biorare.biom"
,
treefilename
=
"biorare.nwk"
)
sample_data
(
biorare
)
<-
sample_data
(
biorare
)
<-
read.table
(
"biorare.tsv"
,
header
=
TRUE
,
row.names
=
1
)
read.table
(
"biorare.tsv"
,
header
=
TRUE
,
row.names
=
1
)
colnames
(
tax_table
(
biorare
))
<-
c
(
"Kingdom"
,
"Phylum"
,
"Class"
,
"Order"
,
"Family"
,
"Genus"
,
"Species"
)
colnames
(
tax_table
(
biorare
))
<-
c
(
"Kingdom"
,
"Phylum"
,
"Class"
,
"Order"
,
"Family"
,
"Genus"
,
"Species"
)
tax_table
(
biorare
)[
grep
(
"unknown "
,
tax_table
(
biorare
))]
<-
NA
tax_table
(
biorare
)[
grep
(
"unknown "
,
tax_table
(
biorare
))]
<-
NA
# cellulose <- import_biom(BIOMfilename = "cellulose.biom")
# cellulose <- import_biom(BIOMfilename = "cellulose.biom")
# sample_data(cellulose) <- read.table("cellulose.tsv", header = TRUE, row.names = 1)
# sample_data(cellulose) <- read.table("cellulose.tsv", header = TRUE, row.names = 1)
save
(
GlobalPatterns
,
food
,
kinetic
,
soil
,
ravel
,
biorare
,
file
=
"demo.RData"
)
# save(GlobalPatterns, food, kinetic, soil, ravel, biorare, file = "demo.RData")
save
(
food
,
file
=
"demo.RData"
)
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