if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("ggtreeExtra")
BiocManager::install("ggtree")
library(ggtreeExtra)
library(ggtree)
library(ggplot2)
library(ggtreeExtra)
library(patchwork)
library(ggridges)
library(phyloseq)
data("GlobalPatterns")
GP <- GlobalPatterns
GP <- prune_taxa(taxa_sums(GP) > 1000, GP)
sample_data(GP)$human <- get_variable(GP, "SampleType") %in%
c("Feces", "Skin")
mergedGP <- merge_samples(GP, "SampleType")
mergedGP <- rarefy_even_depth(mergedGP, rngseed=1024)
mergedGP <- tax_glom(mergedGP,"Order")
melt_simple <- psmelt(mergedGP) %>%
dplyr::filter(Abundance < 120) %>%
dplyr::select(OTU, val=Abundance)
p1 <- ggtree(mergedGP, size = 0.3) +
geom_tippoint(
mapping=aes(color = Phylum),
show.legend = FALSE,
size=0.6
)+
geom_fruit(
data = melt_simple,
geom = geom_density_ridges,
mapping = aes(
y = OTU,
x = val,
fill = Phylum
),
offset = 0.12,
pwidth = 0.4,
lwd = .05,
axis.params = list(
axis = "x",
text.size = 1,
hjust = 0.5,
vjust = 1
),
grid.params = list(),
show.legend = FALSE
)
p1
p1 + layout_circular()
p2 <- ggtree(mergedGP, size = 0.3) +
geom_tippoint(
mapping=aes(color = Phylum),
show.legend = FALSE,
size=0.6
)+
scale_color_viridis_d() +
geom_fruit(
data = melt_simple,
geom = geom_boxplot,
mapping = aes(
y = OTU,
x = val,
fill = Phylum
),
offset = 0.12,
pwidth = 0.4,
size = 0.1,
outlier.size = 0.4,
outlier.stroke = 0.06,
outlier.shape = 21,
axis.params = list(
axis = "x",
text.size = 1,
hjust = 0.5,
vjust = 1
),
grid.params = list(),
show.legend = FALSE
) + scale_fill_viridis_d()
p2
ggsave("./Input/Fig3.jpg",height = 6, width = 8)
p2 + layout_circular()
ggsave("./Input/Fig4.jpg",height = 6, width = 6)