01横向柱形图

构造柱形图的数据集

set.seed(1234)
x <- seq(5,10,by=0.5)

df <- data.frame(`s_Klebsiella_phage_vB_KpnP_SU552A`=sample(x,10,replace=T),
                 `s_Escherichia_phage_ECBP5`=sample(x,10,replace=T),
                 `s_Clostridium_phage_phi8074-B1`=sample(x,10,replace=T),
                 check.names=F)
head(df)

宽格式转换为长格式

library(dplyr)
df %>% reshape2::melt() -> df1

分组求均值和标准差

df %>%
  reshape2::melt() %>%
  group_by(variable) %>%
  summarise(mean_value=mean(value),
            sd_value=sd(value)) -> df2

柱状图叠加误差线和散点图

library(ggplot2)
ggplot() +
  geom_col(data=df2,aes(x=variable,y=mean_value),
           fill="#8babd3",
           color="black") +
  geom_errorbar(data=df2,aes(x=variable,
                             ymin=mean_value-sd_value,
                             ymax=mean_value+sd_value),
                width=0.2) +
  geom_jitter(data=df1,aes(x=variable,y=value),
              width=0.2,color="grey")

image.png

调整坐标，让屁股朝右

ggplot() +
  geom_col(data=df2,aes(x=variable,y=mean_value),
           fill="#8babd3",
           color="black") +
  geom_errorbar(data=df2,aes(x=variable,
                             ymin=mean_value-sd_value+0.001,
                             ymax=mean_value+sd_value),
                width=0.2) +
  geom_jitter(data=df1,aes(x=variable,y=value),
              width=0.2,color="grey") +
  ## scale_y_continuous(expand=c(0,0)) +
  theme_bw() +
  coord_flip() +
  scale_y_reverse(expand=c(0,0),
                  position="right") +
  labs(x=NULL,y=NULL) -> p1

image.png

第二个柱形图也用这个数据

ggplot() +
  geom_col(data=df2,aes(x=variable,y=mean_value),
           fill="#ffc080",
           color="black") +
  geom_errorbar(data=df2,aes(x=variable,
                             ymin=mean_value-sd_value+0.001,
                             ymax=mean_value+sd_value),
                width=0.2) +
  geom_jitter(data=df1,aes(x=variable,y=value),
              width=0.2,color="grey") +
  scale_y_continuous(expand=c(0,0)) +
  theme_bw() +
  coord_flip() +
  labs(x=NULL,y=NULL) +
  theme(axis.text.y=element_blank(),
        axis.ticks.y=element_blank()) -> p2

image.png

构造最右侧的热图数据

df3 <- data.frame(x="A",
                  y=c("s_Klebsiella_phage_vB_KpnP_SU552A",
                      "s_Escherichia_phage_ECBP5",
                      "s_Clostridium_phage_phi8074-B1"),
                  group=c("f_Siphoviridae",
                          "f_Podoviridae",
                          "f_Podoviridae"))

ggplot(df3,aes(x=x,y=y)) +
  geom_tile(aes(fill=group),show.legend=F) +
  labs(x=NULL,y=NULL) +
  scale_x_discrete(expand=c(0,0)) +
  scale_y_discrete(expand=c(0,0),
                   position="right",
                   labels=c("f_Podoviridae","","f_Siphoviridae")) +
  theme(panel.background=element_blank(),
        axis.ticks=element_blank(),
        axis.text.x=element_blank()) +
  scale_fill_manual(values=c("#c65911","#ffd965")) -> p3

image.png

拼图

library(patchwork)
p1+p2+p3+ggtitle("Bacteriophages") +
  theme(plot.title=element_text(hjust=5)) +
  plot_layout(widths=c(1.2,1,0.2)) -> p
ggsave("Rplot.pdf",p,width=10,height=3)

image.png