How to draw this picture | Batch violin plot + box plot + scatter + difference analysis

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[How to draw this picture] The series of pictures are all from VIP群the students' questions. The tweet is only a reproduction of the picture, and does not mean that the author agrees with the form of the picture. Students are welcome to analyze interesting pictures in the group.

Pictures of this issue

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「Title：」Typing characteristics of metabolism-related genes in osteoporosis

「Journal：」Front. Pharmacol.

「Doi：」https://doi.org/10.1016/j.eja.2022.126692
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read picture

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The expression difference box plot represents the difference in expression levels of GPR31, GATM, DDB2, ARMCX1, RPS6, BTBD3, ADAMTSL4, COQ6, B3GNT2, and CD9 genes among the three isoforms.
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Nothing special. The box plot drawn before:

Reproduce results

row1

all

Sample data and code collection

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drawing

# loda data ana preprocess
mRNA <- read.csv("All_mRNA_FPKM.csv",header=T,row.names=1)
#log2
bar_mat <- t(log2(mRNA+1))
# group info
anno <- read.csv("sample_index.csv",header=T,row.names=1)
anno$type2 <- anno$Type
anno <- anno[rownames(bar_mat),]
bar_mat <- bar_mat[rownames(anno),]
bar_mat<- as.data.frame(bar_mat)
bar_mat$sam <- anno$Type

## plot
library(RColorBrewer)
library(ggpubr)
library(ggplot2)
bar_mat$sam<-factor(bar_mat$sam,levels=c("C1","C2","C3","C4"))
# comparisons
my_comparisons <- list(c("C1", "C2"),
                       c("C1", "C3"),
                       c("C1", "C4"))


# gene list
gc <- head( colnames(bar_mat), -1)
#开始批量绘制
plist<-list()
for (i in 1:length(gc)){
  bar_tmp<-bar_mat[,c(gc[i],"sam")]
  colnames(bar_tmp)<-c("Expression","sam")
  pb1<- ggplot(data = bar_tmp,aes(x = sam, 
                                    y = Expression , 
                                    fill = sam))+ 
    scale_fill_manual(values = mycol[c(7,5,3,1)]) +
    geom_violin(alpha = 0.4, position = position_dodge(width = .75), 
                size = 0.8, color="black") +
    geom_boxplot(notch = TRUE, outlier.size = -1, 
                 color="black", lwd=0.8, alpha = 0.7) +
    geom_point(shape = 21, size=2, 
               position = position_jitterdodge(), 
               color="black", alpha = 1) +
    theme_bw() + 
    ylab("Log12(FPKM+1)") +
    xlab(gc[i]) +
    theme(axis.text.x = element_text(size = 12, color = "black"),
          axis.ticks = element_line(size=0.2, color="black"),
          axis.ticks.length = unit(0.2, "cm"),
          legend.position = "none",
          panel.background = element_blank(),
          panel.grid = element_blank(),
          axis.title = element_text(size = 12),
          axis.text = element_text(size = 12)) +
    stat_compare_means(method="t.test",hide.ns = F,comparisons =my_comparisons,label="p.signif")
  plist[[i]]<-pb1
} 

# cowplot
library(cowplot)
p <- plot_grid(plotlist = plist, ncol = 5)
## save
ggsave("boxplot1208.pdf",width = 14,height = 20)

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