# R study (Pyramid plot)
## Pyramid plot drawing
::: info
This is the method to create pyramid plot to distribute gene proportion of B. carinata subgenomes. These plots were produced with R-studio and statements are described as follows.
:::
---
## R-studio statement
### Turn on the required libraries
```r=
library(readxl)
library(ggplot2)
library(ggthemes)
library(forcats)
library(dplyr)
```
### Turn off scientific notations like 1e+40
```r=
options(scipen = 999)
```
### Load raw data
```r=
df<-read_excel("dfdf.xlsx")
```
### Create the gene_content plot
```r=
df %>%
mutate(Assembly = fct_reorder(Assembly, Order)) %>%
ggplot(aes(x = Percentage_of_gene_content_in_each_genome, y = Assembly, fill = Subgenome)) +
geom_bar(stat = "identity", width = .5) +
scale_x_continuous(breaks=seq(-60,60,10),labels=abs(seq(-60,60,10))) +
scale_fill_brewer(palette = "Dark2") +
theme_grey() +
theme(axis.line = element_line(colour = "black")) +
labs(x="Percentage of gene content in each genome", y="Assembly", fill="Subgenome") +
expand_limits(x=c(-65,65))
```
### Create genome_size plot
```r=
df %>%
mutate(Assembly = fct_reorder(Assembly, Order)) %>%
ggplot(aes(x = Percentage_of_genome_size_in_each_genome, y = Assembly, fill = Subgenome)) +
geom_bar(stat = "identity", width = .5) +
scale_x_continuous(breaks=seq(-60,60,10),labels=abs(seq(-60,60,10))) +
scale_fill_brewer(palette = "Dark2") +
theme_grey() +
theme(axis.line = element_line(colour = "black")) +
labs(x="Percentage of genome size in each genome", y="Assembly", fill="Subgenome") +
expand_limits(x=c(-65,65))
```
### Facet grid plot
```r=
df %>%
mutate(Assembly = fct_reorder(Assembly, Order)) %>%
ggplot(aes(x = Xaxis, y = Assembly, fill = Subgenome)) +
geom_bar(stat = "identity", width = .5) + scale_x_continuous(breaks=seq(-60,60,10),labels=abs(seq(-60,60,10))) +
scale_fill_brewer(palette = "Dark2") +
theme_grey() +
theme(axis.line = element_line(colour = "black")) +
labs(x="Xaxis", y="Assembly", fill="Subgenome") +
expand_limits(x=c(-65,65)) + facet_grid(cols=vars(Facet))
```
### Save as PDF
```r=
ggsave("Pyramid.pdf", width = 8, height=6)
```
---
### Reference
-- http://r-statistics.co/Top50-Ggplot2-Visualizations-MasterList-R-Code.html
-- https://www.r-graph-gallery.com/267-reorder-a-variable-in-ggplot2.html
-- https://stackoverflow.com/questions/10861773/remove-grid-background-color-and-top-and-right-borders-from-ggplot2
### input file
### Individual pyramid plot
[Download link](https://pastebin.com/dnrSA80W)
| Order | Taxonomy | Assembly | Sub | Subgenome | Percentage_of_gene_content_in_each_genome | Percentage_of_genome_size_in_each_genome |
|-------|-------------------|----------------|--------------|-----------|-------------------------------------------|------------------------------------------|
| 1 | Brassica carinata | Gomenzer | BC subgenome | Left | -54.3 | -52.39 |
| 1 | Brassica carinata | Gomenzer | Cc subgenome | Right | 45.7 | 47.61 |
| 2 | Brassica carinata | ZD-1 | BC subgenome | Left | -41.75 | -45.37 |
| 2 | Brassica carinata | ZD-1 | Cc subgenome | Right | 58.25 | 54.63 |
| 3 | Brassica juncea | T8466_v1 | Aj subgenome | Left | -50.53 | -47.57 |
| 3 | Brassica juncea | T8466_v1 | Bj subgenome | Right | 49.47 | 52.43 |
| 4 | Brassica juncea | Varuna | Aj subgenome | Left | -45.49 | -38.54 |
| 4 | Brassica juncea | Varuna | Bj subgenome | Right | 54.51 | 61.46 |
| 5 | Brassica napus | Darmor-bzh V5 | An subgenome | Left | -44.23 | -38.42 |
| 5 | Brassica napus | Darmor-bzh V5 | Cn subgenome | Right | 55.77 | 61.58 |
| 6 | Brassica napus | Darmor-bzh V10 | An subgenome | Left | -44.15 | -39.32 |
| 6 | Brassica napus | Darmor-bzh V10 | Cn subgenome | Right | 55.85 | 60.68 |
| 7 | Brassica napus | Express617 | An subgenome | Left | -46.86 | -38.66 |
| 7 | Brassica napus | Express617 | Cn subgenome | Right | 53.14 | 61.34 |
| 8 | Brassica napus | GanganF73 | An subgenome | Left | -45.95 | -41.32 |
| 8 | Brassica napus | GanganF73 | Cn subgenome | Right | 54.05 | 58.68 |
| 9 | Brassica napus | No2127 | An subgenome | Left | -45.53 | -40.75 |
| 9 | Brassica napus | No2127 | Cn subgenome | Right | 54.47 | 59.25 |
| 10 | Brassica napus | QuintaA | An subgenome | Left | -45.2 | -40.48 |
| 10 | Brassica napus | QuintaA | Cn subgenome | Right | 54.8 | 59.52 |
| 11 | Brassica napus | Shengli3 | An subgenome | Left | -46.68 | -41.25 |
| 11 | Brassica napus | Shengli3 | Cn subgenome | Right | 53.32 | 58.75 |
| 12 | Brassica napus | Tapidor3 | An subgenome | Left | -45.14 | -40.81 |
| 12 | Brassica napus | Tapidor3 | Cn subgenome | Right | 54.86 | 59.19 |
| 13 | Brassica napus | Westar | An subgenome | Left | -45.87 | -41.14 |
| 13 | Brassica napus | Westar | Cn subgenome | Right | 54.13 | 58.86 |
| 14 | Brassica napus | Zheyou73 | An subgenome | Left | -46.57 | -40.98 |
| 14 | Brassica napus | Zheyou73 | Cn subgenome | Right | 53.43 | 59.02 |
| 15 | Brassica napus | Zs11 | An subgenome | Left | -45.77 | -40.79 |
| 15 | Brassica napus | Zs11 | Cn subgenome | Right | 54.23 | 59.21 |
#### Facet_grid
| Facet | Order | Taxonomy | Assembly | Sub | Subgenome | Xaxis |
|-------|-------|-------------------|----------------|--------------|-----------|--------|
| 1 | 1 | Brassica carinata | Gomenzer | BC subgenome | Left | -54.3 |
| 1 | 1 | Brassica carinata | Gomenzer | Cc subgenome | Right | 45.7 |
| 1 | 2 | Brassica carinata | ZD-1 | BC subgenome | Left | -41.75 |
| 1 | 2 | Brassica carinata | ZD-1 | Cc subgenome | Right | 58.25 |
| 1 | 3 | Brassica juncea | T8466_v1 | Aj subgenome | Left | -50.53 |
| 1 | 3 | Brassica juncea | T8466_v1 | Bj subgenome | Right | 49.47 |
| 1 | 4 | Brassica juncea | Varuna | Aj subgenome | Left | -45.49 |
| 1 | 4 | Brassica juncea | Varuna | Bj subgenome | Right | 54.51 |
| 1 | 5 | Brassica napus | Darmor-bzh V5 | An subgenome | Left | -44.23 |
| 1 | 5 | Brassica napus | Darmor-bzh V5 | Cn subgenome | Right | 55.77 |
| 1 | 6 | Brassica napus | Darmor-bzh V10 | An subgenome | Left | -44.15 |
| 1 | 6 | Brassica napus | Darmor-bzh V10 | Cn subgenome | Right | 55.85 |
| 1 | 7 | Brassica napus | Express617 | An subgenome | Left | -46.86 |
| 1 | 7 | Brassica napus | Express617 | Cn subgenome | Right | 53.14 |
| 1 | 8 | Brassica napus | GanganF73 | An subgenome | Left | -45.95 |
| 1 | 8 | Brassica napus | GanganF73 | Cn subgenome | Right | 54.05 |
| 1 | 9 | Brassica napus | No2127 | An subgenome | Left | -45.53 |
| 1 | 9 | Brassica napus | No2127 | Cn subgenome | Right | 54.47 |
| 1 | 10 | Brassica napus | QuintaA | An subgenome | Left | -45.2 |
| 1 | 10 | Brassica napus | QuintaA | Cn subgenome | Right | 54.8 |
| 1 | 11 | Brassica napus | Shengli3 | An subgenome | Left | -46.68 |
| 1 | 11 | Brassica napus | Shengli3 | Cn subgenome | Right | 53.32 |
| 1 | 12 | Brassica napus | Tapidor3 | An subgenome | Left | -45.14 |
| 1 | 12 | Brassica napus | Tapidor3 | Cn subgenome | Right | 54.86 |
| 1 | 13 | Brassica napus | Westar | An subgenome | Left | -45.87 |
| 1 | 13 | Brassica napus | Westar | Cn subgenome | Right | 54.13 |
| 1 | 14 | Brassica napus | Zheyou73 | An subgenome | Left | -46.57 |
| 1 | 14 | Brassica napus | Zheyou73 | Cn subgenome | Right | 53.43 |
| 1 | 15 | Brassica napus | Zs11 | An subgenome | Left | -45.77 |
| 1 | 15 | Brassica napus | Zs11 | Cn subgenome | Right | 54.23 |
| 2 | 1 | Brassica carinata | Gomenzer | BC subgenome | Left | -52.39 |
| 2 | 1 | Brassica carinata | Gomenzer | Cc subgenome | Right | 47.61 |
| 2 | 2 | Brassica carinata | ZD-1 | BC subgenome | Left | -45.37 |
| 2 | 2 | Brassica carinata | ZD-1 | Cc subgenome | Right | 54.63 |
| 2 | 3 | Brassica juncea | T8466_v1 | Aj subgenome | Left | -47.57 |
| 2 | 3 | Brassica juncea | T8466_v1 | Bj subgenome | Right | 52.43 |
| 2 | 4 | Brassica juncea | Varuna | Aj subgenome | Left | -38.54 |
| 2 | 4 | Brassica juncea | Varuna | Bj subgenome | Right | 61.46 |
| 2 | 5 | Brassica napus | Darmor-bzh V5 | An subgenome | Left | -38.42 |
| 2 | 5 | Brassica napus | Darmor-bzh V5 | Cn subgenome | Right | 61.58 |
| 2 | 6 | Brassica napus | Darmor-bzh V10 | An subgenome | Left | -39.32 |
| 2 | 6 | Brassica napus | Darmor-bzh V10 | Cn subgenome | Right | 60.68 |
| 2 | 7 | Brassica napus | Express617 | An subgenome | Left | -38.66 |
| 2 | 7 | Brassica napus | Express617 | Cn subgenome | Right | 61.34 |
| 2 | 8 | Brassica napus | GanganF73 | An subgenome | Left | -41.32 |
| 2 | 8 | Brassica napus | GanganF73 | Cn subgenome | Right | 58.68 |
| 2 | 9 | Brassica napus | No2127 | An subgenome | Left | -40.75 |
| 2 | 9 | Brassica napus | No2127 | Cn subgenome | Right | 59.25 |
| 2 | 10 | Brassica napus | QuintaA | An subgenome | Left | -40.48 |
| 2 | 10 | Brassica napus | QuintaA | Cn subgenome | Right | 59.52 |
| 2 | 11 | Brassica napus | Shengli3 | An subgenome | Left | -41.25 |
| 2 | 11 | Brassica napus | Shengli3 | Cn subgenome | Right | 58.75 |
| 2 | 12 | Brassica napus | Tapidor3 | An subgenome | Left | -40.81 |
| 2 | 12 | Brassica napus | Tapidor3 | Cn subgenome | Right | 59.19 |
| 2 | 13 | Brassica napus | Westar | An subgenome | Left | -41.14 |
| 2 | 13 | Brassica napus | Westar | Cn subgenome | Right | 58.86 |
| 2 | 14 | Brassica napus | Zheyou73 | An subgenome | Left | -40.98 |
| 2 | 14 | Brassica napus | Zheyou73 | Cn subgenome | Right | 59.02 |
| 2 | 15 | Brassica napus | Zs11 | An subgenome | Left | -40.79 |
| 2 | 15 | Brassica napus | Zs11 | Cn subgenome | Right | 59.21 |
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