The graph drawn in this tutorial is from the NC journal. I don’t know what the graph is called, but if you look closely, it belongs to the “ringed histogram”, so that’s what it’s called!
It looks relatively new, so let’s learn it! !
Drawing
Load R package
library(ggplot2)
Load data
Draw basic graphics
p <- ggplot(data, aes(x=as.factor(id), y=est, fill=group)) + # Note that id is a factor. If x is numeric, there is some space between the first bar geom_bar(aes(x=as.factor(id), y=est, fill=group), stat="identity", alpha=1) + geom_errorbar(aes(ymin = est-se, ymax = est + se), width = 0.2, position = position_dodge(.9), size = .5, alpha=1)
Add a val
p2 <- p + geom_segment(data=grid_data, aes(x = end, y = 1, xend = start, yend = 1), color = "grey", alpha=1, size=0.3 , inherit.aes = FALSE ) + geom_segment(data=grid_data, aes(x = end, y = 0.8, xend = start, yend = 0.8), color = "grey", alpha=1, size=0.3 , inherit.aes = FALSE ) + geom_segment(data=grid_data, aes(x = end, y = 0.6, xend = start, yend = 0.6), color = "grey", alpha=1, size=0.3 , inherit.aes = FALSE ) + geom_segment(data=grid_data, aes(x = end, y = 0.4, xend = start, yend = 0.4), color = "grey", alpha=1, size=0.3 , inherit.aes = FALSE ) + geom_segment(data=grid_data, aes(x = end, y = 0.2, xend = start, yend = 0.2), color = "grey", alpha=1, size=0.3 , inherit.aes = FALSE ) + geom_segment(data=grid_data, aes(x = end, y = 0, xend = start, yend = 0), color = "grey", alpha=1, size=0.3 , inherit.aes = FALSE )
Add numbers to val
p3 <- p2 +
annotate("text", x = rep(max(data$id),6), y = c(0, 0.2, 0.4, 0.6, 0.8, 1),
label = c("0", "0.2", "0.4", "0.6", "0.8", "1") , color="black", size =4 , angle=0, hjust=1)
Extend the y-axis
p4 <- p3 + geom_bar(aes(x=as.factor(id), y=est, fill=group), stat="identity", alpha=0.5) + ylim(-1,3)
Beautify
p5 <- p4 +
theme_minimal() +
theme(
legend.position = "right",
legend.title = element_blank(),
legend.text = element_text(size=12),
axis.text = element_blank(),
axis.title = element_blank(),
panel. grid = element_blank())
Changes into a circular shape
Use the coord_polar() function to convert
p6 <- p5 + coord_polar()
Color beautification
p7 <- p6 + scale_fill_manual(breaks = c("Intellectual disabilities",
"Communication disorders",
"ASD",
"ADHD",
"Specific learning disorders",
"Dyslexia-related phenotypes",
"Dysgraphia-related phenotypes",
"Dyscalculia-related phenotypes",
"Motor disorders"),
values = c("#184e77","#1e6091","#1a759f",
"#168aad","#34a0a4","#52b69a",
"#76c893","#99d98c","#b5e48c")) +
ggtitle("Heritability of sub-categories of Neurodevelopmental Disorders")
The label is mapped to the column
p8 <- p7 +
geom_text(data=label_data, aes(x=id, y= est + se + 0.2, label=pheno, hjust=hjust),
color="black", alpha=1, size=4, angle= label_data$angle, inherit.aes = FALSE )
Complete code
ggplot(data, aes(x=as.factor(id), y=est, fill=group)) + # Note that id is a factor. If x is numeric, there is some space between the first bar
geom_bar(aes(x=as.factor(id), y=est, fill=group), stat="identity", alpha=1) +
geom_errorbar(aes(ymin = est-se, ymax = est + se), width = 0.2, position = position_dodge(.9), size = .5, alpha=1) +
# add val
geom_segment(data=grid_data, aes(x = end, y = 1, xend = start, yend = 1), color = "grey", alpha=1, size=0.3 , inherit.aes = FALSE ) +
geom_segment(data=grid_data, aes(x = end, y = 0.8, xend = start, yend = 0.8), color = "grey", alpha=1, size=0.3 , inherit.aes = FALSE ) +
geom_segment(data=grid_data, aes(x = end, y = 0.6, xend = start, yend = 0.6), color = "grey", alpha=1, size=0.3 , inherit.aes = FALSE ) +
geom_segment(data=grid_data, aes(x = end, y = 0.4, xend = start, yend = 0.4), color = "grey", alpha=1, size=0.3 , inherit.aes = FALSE ) +
geom_segment(data=grid_data, aes(x = end, y = 0.2, xend = start, yend = 0.2), color = "grey", alpha=1, size=0.3 , inherit.aes = FALSE ) +
geom_segment(data=grid_data, aes(x = end, y = 0, xend = start, yend = 0), color = "grey", alpha=1, size=0.3 , inherit.aes = FALSE ) +
# add the numbers in val
annotate("text", x = rep(max(data$id),6), y = c(0, 0.2, 0.4, 0.6, 0.8, 1),
label = c("0", "0.2", "0.4", "0.6", "0.8", "1") , color="black", size =4 , angle=0, hjust=1) +
geom_bar(aes(x=as.factor(id), y=est, fill=group), stat="identity", alpha=0.5) +
ylim(-1,3) +
theme_minimal() +
theme(
legend.position = "right",
legend.title = element_blank(),
legend.text = element_text(size=12),
axis.text = element_blank(),
axis.title = element_blank(),
panel.grid = element_blank()) +
## change ring
coord_polar() +
## Column annotation
scale_fill_manual(breaks = c("Intellectual disabilities",
"Communication disorders",
"ASD",
"ADHD",
"Specific learning disorders",
"Dyslexia-related phenotypes",
"Dysgraphia-related phenotypes",
"Dyscalculia-related phenotypes",
"Motor disorders"),
## column color
values = c("#184e77","#1e6091","#1a759f",
"#168aad","#34a0a4","#52b69a",
"#76c893","#99d98c","#b5e48c")) +
ggtitle("Heritability of sub-categories of Neurodevelopmental Disorders") +
## Map labels to columns
geom_text(data=label_data, aes(x=id, y= est + se + 0.2, label=pheno, hjust=hjust),
color="black", alpha=1, size=4, angle= label_data$angle, inherit.aes = FALSE )
ENDING!
Previous articles:
1. The most complete WGCNA tutorial (replace the data to get all the results and graphics)
WGCNA Analysis | Whole Process Analysis Code | Code 1
WGCNA Analysis | Whole Process Analysis Code | Code 2
WGCNA Analysis | Whole Process Code Sharing | Code Three
2. Beautiful graphics drawing tutorial
Beautiful graphics drawing tutorial
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Xiao Du’s life letter notes, which mainly publish or include bioinformatics tutorials, as well as R-based analysis and visualization (including data analysis, graph drawing, etc.); share interested literature and learning materials!!