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Commit 652c7370 authored by magali's avatar magali
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fichiers html rmd et figures png f6w

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202110_BALBc/Pool_cohortes/report_pool_F6w.Rmd
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......@@ -287,7 +287,7 @@ p1 <- ggplot(plotdata,aes(x = Group,y=Abundance, color = Group, Group = Group))
## Compare reference level T0 to all other levels using a wilcoxon test and adjust p-values using the holm correction.
p1 <- p1 + stat_compare_means(aes(label = ..p.signif..), method = "wilcox.test", p.adjust.method = "holm", ref.group = "S-A_F3w", hide.ns = T,
p1 <- p1 + stat_compare_means(aes(label = ..p.signif..), method = "wilcox.test", p.adjust.method = "holm", ref.group = "S-A_F6w", hide.ns = T,
label.y.npc = c(0.90),
size = 7,
fontface = "bold")
......@@ -318,7 +318,7 @@ p2 <- ggplot(plotdata,aes(x = Group,y=Abundance, color = Group, Group = Group))
theme(axis.text.x = element_text(angle = 45, hjust = 1, size = 10))
## Compare reference level T0 to all other levels using a wilcoxon test and adjust p-values using the holm correction.
p2 <- p2 + stat_compare_means(aes(label = ..p.signif..), method = "wilcox.test", p.adjust.method = "holm", ref.group = "S-AG_F3w", hide.ns = T,
p2 <- p2 + stat_compare_means(aes(label = ..p.signif..), method = "wilcox.test", p.adjust.method = "holm", ref.group = "S-AG_F6w", hide.ns = T,
label.y.npc = c(0.90),
size = 7,
fontface = "bold")
......@@ -517,7 +517,7 @@ p3 <- ggplot(plotdata,aes(x = Group,y=Abundance, color = Group, Group = Group))
## Compare reference level T0 to all other levels using a wilcoxon test and adjust p-values using the holm correction.
p3 <- p3 + stat_compare_means(aes(label = ..p.signif..), method = "wilcox.test", p.adjust.method = "holm", ref.group = "S-A_F3w", hide.ns = T,
p3 <- p3 + stat_compare_means(aes(label = ..p.signif..), method = "wilcox.test", p.adjust.method = "holm", ref.group = "S-A_F6w", hide.ns = T,
label.y.npc = c(0.90),
size = 7,
fontface = "bold")
......@@ -548,7 +548,7 @@ p4 <- ggplot(plotdata,aes(x = Group,y=Abundance, color = Group, Group = Group))
theme(axis.text.x = element_text(angle = 45, hjust = 1, size = 10))
## Compare reference level T0 to all other levels using a wilcoxon test and adjust p-values using the holm correction.
p4 <- p4 + stat_compare_means(aes(label = ..p.signif..), method = "wilcox.test", p.adjust.method = "holm", ref.group = "S-AG_F3w", hide.ns = T,
p4 <- p4 + stat_compare_means(aes(label = ..p.signif..), method = "wilcox.test", p.adjust.method = "holm", ref.group = "S-AG_F6w", hide.ns = T,
label.y.npc = c(0.90),
size = 7,
fontface = "bold")
......@@ -1067,10 +1067,10 @@ family.palette<- c("S-A" = "#A2E06F",
p <- plot_ordination(frogs.data.rare, ord, color = "Group_bis")
p <- p + theme_bw() + ggtitle("MDS + Bray Curtis")+ scale_color_manual(values = family.palette)
p <- p +geom_point(size=2)+ stat_ellipse(aes(group = Group_bis), size = 1)+
annotate(geom="text", x=0.5, y = 0.3, label = "S-A", size = 5, color = "#A2E06F")+
annotate(geom="text", x=0.3, y = 0.3, label = "S-A", size = 5, color = "#A2E06F")+
annotate(geom="text", x=0.35, y = 0, label = "A", size = 5, color = "#6FC1E0")+
annotate(geom="text", x=-0.5, y = -0.10, label = "S-AG", size = 5, color = "#227432")+
annotate(geom="text", x=0, y = -0.5, label = "AG", size = 5, color = "#8C67A9")
annotate(geom="text", x=-0.5, y = -0.20, label = "S-AG", size = 5, color = "#227432")+
annotate(geom="text", x=0, y = -0.4, label = "AG", size = 5, color = "#8C67A9")
plot(p)
```
......@@ -1109,10 +1109,10 @@ ord <- ordinate(frogs.data.rare, method = "MDS", distance = "cc")
p <- plot_ordination(frogs.data.rare, ord, color = "Group_bis")
p <- p + theme_bw() + ggtitle("MDS + Jaccard")+ scale_color_manual(values = family.palette)
p <- p +geom_point(size=2)+ stat_ellipse(aes(group = Group_bis), size = 1)+
annotate(geom="text", x=0.4, y = -0.4, label = "S-A", size = 5, color = "#A2E06F")+
annotate(geom="text", x=0.35, y = 0, label = "A", size = 5, color = "#6FC1E0")+
annotate(geom="text", x=-0.5, y = -0.10, label = "S-AG", size = 5, color = "#227432")+
annotate(geom="text", x=-0.25, y = 0.2, label = "AG", size = 5, color = "#8C67A9")
annotate(geom="text", x=0.2, y = -0.4, label = "S-A", size = 5, color = "#A2E06F")+
annotate(geom="text", x=0.3, y = 0, label = "A", size = 5, color = "#6FC1E0")+
annotate(geom="text", x=-0.45, y = -0.10, label = "S-AG", size = 5, color = "#227432")+
annotate(geom="text", x=-0.3, y = 0.2, label = "AG", size = 5, color = "#8C67A9")
plot(p)
......@@ -1134,9 +1134,9 @@ p <- plot_ordination(frogs.data.rare, ord, color = "Group_bis")
p <- p + theme_bw() + ggtitle("MDS + Unifrac")+ scale_color_manual(values = family.palette)
p <- p +geom_point(size=2)+ stat_ellipse(aes(group = Group_bis), size = 1)+
annotate(geom="text", x=0.1, y = -0.2, label = "S-A", size = 5, color = "#A2E06F")+
annotate(geom="text", x=0.25, y = 0, label = "A", size = 5, color = "#6FC1E0")+
annotate(geom="text", x=-0.3, y = -0.10, label = "S-AG", size = 5, color = "#227432")+
annotate(geom="text", x=-0.1, y = 0.2, label = "AG", size = 5, color = "#8C67A9")
annotate(geom="text", x=0.21, y = 0, label = "A", size = 5, color = "#6FC1E0")+
annotate(geom="text", x=-0.28, y = -0.10, label = "S-AG", size = 5, color = "#227432")+
annotate(geom="text", x=-0.2, y = 0.2, label = "AG", size = 5, color = "#8C67A9")
plot(p)
......@@ -1160,7 +1160,7 @@ p <- p +geom_point(size=2)+ stat_ellipse(aes(group = Group_bis), size = 1)+
annotate(geom="text", x=0.1, y = -0.22, label = "S-A", size = 5, color = "#A2E06F")+
annotate(geom="text", x=0.25, y = 0.08, label = "A", size = 5, color = "#6FC1E0")+
annotate(geom="text", x=-0.3, y = -0.15, label = "S-AG", size = 5, color = "#227432")+
annotate(geom="text", x=0.08, y = 0.2, label = "AG", size = 5, color = "#8C67A9")
annotate(geom="text", x=0.01, y = 0.2, label = "AG", size = 5, color = "#8C67A9")
plot(p)
......
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