论文
Large variation in the association between seasonal antibiotic use and resistance across multiple bacterial species and antibiotic classes
数据代码链接
https://github.com/orgs/gradlab/repositories
今天的推文重复一下论文中的 Figure 3A
image.png
今天的推文主要有两个知识点
- 一个是坐标轴文字同时存在斜体字和正常字应该怎么处理（上图的横坐标）
- 二是坐标轴标题如果要换行应该怎么处理（上图的纵坐标）
准备作图数据的代码
library(readr)
library(tidyverse)
res.modelA.params <- read_csv("use-resistance-seasonality/tables/resistance_modelA_values.csv")
filter_models_AIC_func = function(table, group_cols) {
table.fil = table %>%
group_by_at(vars(all_of(group_cols))) %>%
mutate(rank = dense_rank(AIC)) %>%
ungroup() %>%
filter(rank == 1) %>%
select(-AIC, -rank)
return(table.fil)
}
res.modelA.params.fil <- filter_models_AIC_func(res.modelA.params, c("organism", "drug_name"))
f3a_data <- res.modelA.params.fil %>%
filter(term == "amplitude") %>%
mutate(org_drug = paste(organism, drug_code, sep = "/")) %>%
select(org_drug, drug_class, period, term, estimate, ci.lower, ci.upper)
准备作图配色
colors <- setNames(c("#220050", "#b30059","#0091a8","#359023", "#ffa500"),
c("Macrolides", "Nitrofurans", "Penicillins", "Quinolones", "Tetracyclines"))
定义横坐标文字标签
这里设置斜体使用expression()函数
labs <- c("S. aureus/CIP" = expression(paste(italic("S. aureus"), " / CIP")),
"S. aureus/ERY" = expression(paste(italic("S. aureus"), " / ERY")),
"S. aureus/NIT" = expression(paste(italic("S. aureus"), " / NIT")),
"S. aureus/OXA" = expression(paste(italic("S. aureus"), " / OXA")),
"S. aureus/PEN" = expression(paste(italic("S. aureus"), " / PEN")),
"S. aureus/TET" = expression(paste(italic("S. aureus"), " / TET")),
"E. coli/AMC" = expression(paste(italic("E. coli"), " / AMC")),
"E. coli/AMP" = expression(paste(italic("E. coli"), " / AMP")),
"E. coli/CIP" = expression(paste(italic("E. coli"), " / CIP")),
"E. coli/NIT" = expression(paste(italic("E. coli"), " / NIT")),
"E. coli/TET" = expression(paste(italic("E. coli"), " / TET")),
"K. pneumoniae/AMC" = expression(paste(italic("K. pneumoniae"), " / AMC")),
"K. pneumoniae/CIP" = expression(paste(italic("K. pneumoniae"), " / CIP")),
"K. pneumoniae/NIT" = expression(paste(italic("K. pneumoniae"), " / NIT")),
"K. pneumoniae/TET" = expression(paste(italic("K. pneumoniae"), " / TET")))
画图代码
f3a <- f3a_data %>%
ggplot(aes(x = reorder(org_drug, estimate), y = estimate, color = drug_class)) +
geom_point(size = 2) +
geom_errorbar(aes(ymin = ci.lower, ymax = ci.upper), width = 0.4) +
geom_hline(yintercept = 0, color = "grey20", linetype = "dashed") +
scale_y_continuous(breaks = c(0, 0.05, 0.1), limits = c(-0.02, 0.1)) +
scale_x_discrete(labels = labs) +
scale_color_manual(values = colors, name = "Antibiotic Class") +
ylab(expression(atop("Amplitude of seasonality", "(" ~ log["2"] ~ "(MIC) deviates)"))) +
theme_minimal() +
theme(
axis.title.x = element_blank(),
axis.title.y = element_text(size = 10),
axis.text.x = element_text(size = 10, angle = 45, hjust = 1, vjust = 1),
axis.text.y = element_text(size = 10),
legend.title = element_text(size = 9, face = "bold"),
legend.text = element_text(size = 9),
)
f3a
image.png
纵坐标轴标题换行的代码是ylab()这一行 expression(atop())，如果要换行就把不同的字符串用逗号分开，可以试下如下代码的效果
ggplot()+
geom_point(aes(x=1,y=1))+
ylab(expression(atop("ABCDE"," abcde" ~ "(" ~ ")")))
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