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Magali Monnoye
Analyses_16S
Commits
4fa03b0c
Commit
4fa03b0c
authored
Nov 17, 2021
by
Magali Monnoye
Browse files
fichier rmd et html
parent
037e95d4
Pipeline
#44598
passed with stage
in 3 minutes and 17 seconds
Changes
2
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1
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202111_Rotenone/report_Rotenone.Rmd
View file @
4fa03b0c
...
...
@@ -381,7 +381,7 @@ qsub -cwd -V -N affiliations_stats_cleaned -o LOGS -e LOGS -b y "conda activate
```
Numéro du job **affiliations_stats_cleaned** sur le cluster de migale: 404
8514
Numéro du job **affiliations_stats_cleaned** sur le cluster de migale: 404
9992
Lien vers le [rapport affiliations_stats_cleaned](FROGS/affiliations_stats_cleaned.html)
...
...
@@ -401,7 +401,7 @@ qsub -cwd -V -N tree -o LOGS -e LOGS -b y "conda activate frogs-3.2.2 && tree.py
```
Num
é
ro
du
job
**
tree
**
sur
le
cluster
de
migale
:
404
8515
Num
é
ro
du
job
**
tree
**
sur
le
cluster
de
migale
:
404
9993
Lien
vers
l
'arbre [Tree](FROGS/tree.html)
...
...
@@ -484,7 +484,7 @@ sample_variables(frogs.data)
```{r sample selection,fig.width=10,fig.height=4, eval=TRUE}
#Je supprime les échantillons TF51_2, T026, TF50_2 et T023_2 qui ont un nombre de séquences < 5000
frogs.data <- subset_samples(frogs.data, !(sample_names(frogs.data) %in% c("2
.
1")) )
frogs.data <- subset_samples(frogs.data, !(sample_names(frogs.data) %in% c("2
_
1")) )
frogs.data
```
...
...
@@ -1829,7 +1829,7 @@ plot_da_boxplot(plotdata)
Repr
é
sentation
en
boxplot
des
OTUs
differentiellements
abondants
```{
r
43
-
boxplot
-
Phylum
,
fig
.
width
=
8
,
fig
.
height
=
4
,
eval
=
TRUE
}
```{
r
43
-
boxplot
-
Phylum
,
fig
.
width
=
10
,
fig
.
height
=
4
,
eval
=
TRUE
}
p
<-
ggplot
(
plotdata
,
aes
(
x
=
OTU2
,
y
=
Abundance
,
fill
=
Phylum
,
color
=
Phylum
,
alpha
=
Group
))
+
scale_y_log10
()
+
...
...
@@ -1845,7 +1845,7 @@ plot(p)
###
Boxplot
Family
```{
r
44
-
boxplot
-
Family
,
fig
.
width
=
8
,
fig
.
height
=
4
,
eval
=
TRUE
}
```{
r
44
-
boxplot
-
Family
,
fig
.
width
=
10
,
fig
.
height
=
4
,
eval
=
TRUE
}
p
<-
ggplot
(
plotdata
,
aes
(
x
=
OTU2
,
y
=
Abundance
,
fill
=
Family
,
color
=
Family
,
alpha
=
Group
))
+
scale_y_log10
()
+
scale_alpha_discrete
(
range
=
c
(
0
,
1
),
guide
=
guide_legend
(
override
.
aes
=
list
(
fill
=
"black"
)))
+
...
...
@@ -1880,7 +1880,6 @@ plot_da_compositebis(da.otus, data, labvec = c("Vehicule" = "V", "Rotenone" = "R
```
```{
r
session
info
,
eval
=
TRUE
}
#
conflicts
(
detail
=
TRUE
)
sessionInfo
()
...
...
202111_Rotenone/report_Rotenone.html
View file @
4fa03b0c
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