how to make boxplot of specific row with group of sample in R

Question

I am a new baby in R, I would like to ask for help to make the boxplot with the group I have 2 files, file 1 is the value of the samples (gene expression) test.txt

gene	group1.1	group1.2	group2.1	group2.2
a1	12	13	12	12
a2	2	3	25	31
a3	24	30	34	22
a4	10	11	23	24

and file 2 is the sample design design.txt

file	condition
group1.1	group1
group1.2	group1
group2.1	group2
group2.2	group2

I want to make the boxplot in R with one specific row for example: a1 and have 2 groups 1, and 2; the output looks like boxplot-a1

How can I do this, direct from 2 files? I think I do the stupid way

dt1 <- read.delim("test.txt", sep="\t", header = TRUE)
dg <- read.delim("design.txt", sep="\t", header = TRUE)

I make the new file by copy and transpose:

gene	name	group	expression
a1	Group1.1	group1	12
a1	Group1.2	group1	13
a1	Group2.1	group2	12
a1	Group2.2	group2	12.5
a2	Group1.1	group1	2
a2	Group1.2	group1	3
a2	Group2.1	group2	25
a2	Group2.2	group2	31

    dt <- read.delim("test_t.csv", sep="\t", header = TRUE)

    a1 <- dt[dt$gene %in% "a1",]
    ggplot(a1, aes(x=a1$group, y=a1$expression)) + 
       labs(title = "Expression A1", x = "Group", y = "Expression") +
       stat_boxplot(geom = "errorbar", width = 0.15) + 
        geom_boxplot()

Thank you so much for your help!

Answer 1

Having such data, it is worth first converting the variables of the chr type to factor.

library(tidyverse)

df = read.table(
  header = TRUE,text="
  gene  name    group   expression
a1  Group1.1    group1  12
a1  Group1.2    group1  13
a1  Group2.1    group2  12
a1  Group2.2    group2  12.5
a2  Group1.1    group1  2
a2  Group1.2    group1  3
a2  Group2.1    group2  25
a2  Group2.2    group2  31") %>% 
  as_tibble() %>% 
  mutate(
    gene = gene %>% fct_inorder(),
    name = name %>% fct_inorder(),
    group = group %>% fct_inorder()
  )

Now you can make a boxplot for one value of the gene variable

df %>% filter(gene == "a1") %>% 
  ggplot(aes(gene, expression))+
  geom_boxplot()

Either for both values at once

df %>%
  ggplot(aes(gene, expression, fill=gene))+
  geom_boxplot()