Commit 4fa03b0c authored by Magali Monnoye's avatar Magali Monnoye
Browse files

fichier rmd et html

parent 037e95d4
Pipeline #44598 passed with stage
in 3 minutes and 17 seconds
......@@ -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: 4048514
Numéro du job **affiliations_stats_cleaned** sur le cluster de migale: 4049992
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
```
Numéro du job **tree** sur le cluster de migale: 4048515
Numéro du job **tree** sur le cluster de migale: 4049993
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)
Représentation 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()
......
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