表1：做箱圖
df = read.table("phylum_abundance.txt", header=T, sep="\t", row.names=1)
df$Phylum = rownames(df)
## boxplot
# BGI cohort
input = melt(df, id='Phylum')
input$Phylum = factor(input$Phylum, levels = unique(input$Phylum))
表2：做柱形圖
# CGR2
cgr = read.table("phylum_abundace_cgr2.txt", header=T, sep="\t")
cgr$Phylum = factor(cgr$Phylum, levels = unique(cgr$Phylum))
X軸配色
# X color
col_text = c(rep("indianred3", 7), rep("deepskyblue3", 11))
segment和配色
# segment data
seg = data.frame(Phylum = cgr$Phylum, no = c(1:18))
seg$x_start = seg$no - 0.5
seg$x_end = seg$no + 0.5
col_set = col_text
names(col_set) <- seg$Phylum
seg$Phylum = factor(seg$Phylum, levels = unique(seg$Phylum))
ggplot boxplot barplot segment
ggplot(NULL, aes(x, y)) +
theme_classic() +
geom_boxplot(input, mapping=aes(x=Phylum, y=value*100),
color = "deepskyblue3",
position = position_nudge(x = -0.2),
width = 0.3,
outlier.color = NA,
lwd = 1) +
geom_point(input, mapping=aes(x=Phylum, y=value*100),
pch = 19, color = "deepskyblue3",
size = 0.2,
position = position_nudge(x = -0.2)) +
geom_bar(cgr, mapping=aes(x=Phylum, y=num*100),
stat="identity", width = 0.3,
color = "indianred3",
fill = "white", lwd = 1,
position = position_nudge(x = 0.2)) +
labs(x="", y="Relative abundance (%)") +
theme(panel.grid = element_line(colour = 'white')) +
theme(axis.title = element_text(size = 18),
axis.text = element_text(size = 10),
axis.line = element_line(size = 1),
axis.ticks = element_line(size = 1)) +
theme(axis.text.x = element_text(angle = 60, hjust = 1,
color = col_text)) +
scale_y_continuous(limits=c(0, 100), expand = c(0, 0)) +
geom_segment(seg, mapping=aes(
x = x_start,
y = 100,
xend = x_end,
yend = 100,
color = Phylum), size = 2) +
scale_color_manual(values = col_set) +
theme(legend.position = "none")
ggsave(p, filename="merge2.pdf", width = 12)
ggsave(p, filename="merge.png", width = 8)
