Griding ggplot object in r

Question

I have this data frame

head(d)

# A tibble: 6 x 3
  gene  variable       value
1 CCT5  Res_immune     10.6 
2 CCT5  Non_res_immune 10.5 
3 CDK1  Res_immune      9.25
4 CXCL5 Non_res_immune  9.82
5 GBP1  Res_immune      9.04
6 GBP1  Non_res_immune  9.43
> 

And this code

library(ggplot2)
library(ggrepel)
ggplot(d, aes(x = variable, y = value, fill = variable, label = gene))+
  geom_boxplot(alpha = 0.2)+
  geom_point(position = position_jitter(width = 0.2, seed = 2), show.legend = FALSE)+
  geom_text_repel(position = position_jitter(0.2, seed = 2), show.legend = FALSE)

The genes in first column are involved in cytokine signaling pathway in two groups of patients

This is my plot

I have another data frame for genes in IL17 signaling in the sample patients like

head(d)

# A tibble: 6 x 3
  gene  variable       value
  <chr> <chr>          <dbl>
1 CDK6  Res_immune     17.6 
2 IL6  Non_res_immune 14.5 
3 CXCL8  Res_immune      1.25

How I can put plots from both data in a grade like below where the name of pathways shown instead of DEL, INS, SNP and total like below picture?

Answer 1

What you are looking for is facetting. Using this key word on any search engines you will find dozen of answers describing its use: https://ggplot2.tidyverse.org/reference/facet_grid.html and https://ggplot2.tidyverse.org/reference/facet_wrap.html

To prepare the faceting in ggplot2, a possible way is to bind both dataframes together by first specifying which group they belong such as:

cytokine$Group = "Cytokine"
il17$Group = "IL17"
DF <- rbind(cytokine,il17)
DF

    gene       variable value    Group
1:  CCT5     Res_immune 10.60 Cytokine
2:  CCT5 Non_res_immune 10.50 Cytokine
3:  CDK1     Res_immune  9.25 Cytokine
4: CXCL5 Non_res_immune  9.82 Cytokine
5:  GBP1     Res_immune  9.04 Cytokine
6:  GBP1 Non_res_immune  9.43 Cytokine
7:  CDK6     Res_immune 17.60     IL17
8:   IL6 Non_res_immune 14.50     IL17
9: CXCL8     Res_immune  1.25     IL17

Then, use facet_grid function of ggplot2:

library(ggplot2)
library(ggrepel)
ggplot(DF, aes(x = variable, y = value, fill = variable, label = gene))+
  geom_boxplot(alpha = 0.2)+
  geom_point(position = position_jitter(width = 0.2, seed = 2), show.legend = FALSE)+
  geom_text_repel(position = position_jitter(0.2, seed = 2), show.legend = FALSE)+
  facet_grid(Group~., scales = "free")

Alternatively, you can use facet_grid (or facet_wrap) to have your plot in a single row:

library(ggplot2)
library(ggrepel)
ggplot(DF, aes(x = variable, y = value, fill = variable, label = gene))+
  geom_boxplot(alpha = 0.2)+
  geom_point(position = position_jitter(width = 0.2, seed = 2), show.legend = FALSE)+
  geom_text_repel(position = position_jitter(0.2, seed = 2), show.legend = FALSE)+
  facet_wrap(.~Group, scales = "free")

Reproducible data example

structure(list(gene = c("CCT5", "CCT5", "CDK1", "CXCL5", "GBP1", 
"GBP1"), variable = c("Res_immune", "Non_res_immune", "Res_immune", 
"Non_res_immune", "Res_immune", "Non_res_immune"), value = c(10.6, 
10.5, 9.25, 9.82, 9.04, 9.43), Group = c("Cytokine", "Cytokine", 
"Cytokine", "Cytokine", "Cytokine", "Cytokine")), row.names = c(NA, 
-6L), class = c("data.table", "data.frame"), .internal.selfref = <pointer: 0x55bfc0db9350>)

and

structure(list(gene = c("CDK6", "IL6", "CXCL8"), variable = c("Res_immune", 
"Non_res_immune", "Res_immune"), value = c(17.6, 14.5, 1.25), 
    Group = c("IL17", "IL17", "IL17")), row.names = c(NA, -3L
), class = c("data.table", "data.frame"), .internal.selfref = <pointer: 0x55bfc0db9350>)