boxplot for single value containing data

Question

i have a dataframe where gene names are the column headers and sample names as rownames. they have one value for every cell. example:

           G1         G2       G3
S1  0.19021657  0.129541639 0.741696359
S2  0.431098317 0.791633452 0.502163442
S3  0.433107132 0.085196075 0.071400934
S4  0.800781053 0.221191986 0.918588422

I would like to do a boxplot for every column (gene) - all plotted on one graph.

I tried to reshape the dataframe and then use ggplot, but I couldnt achieve the desired result. is there an elegant way to do this with ggplot?

Your title and description is a bit confusing `I would like to do a boxplot for every column`. Do you need boxplot by column? — akrun, Oct 21 '21 at 17:07

score 2 · Answer 1 · answered Oct 21 '21 at 17:05

2

We can just use boxplot from base R on a data.frame. By default, it gives the boxplot for each columns of the dataset

boxplot(df1)

data

df1 <- structure(list(G1 = c(0.19021657, 0.431098317, 0.433107132, 0.800781053
), G2 = c(0.129541639, 0.791633452, 0.085196075, 0.221191986), 
    G3 = c(0.741696359, 0.502163442, 0.071400934, 0.918588422
    )), class = "data.frame", row.names = c("S1", "S2", "S3", 
"S4"))

answered Oct 21 '21 at 17:05

akrun

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thanks. I was able to do this, however, we will need to convert the plots into html format, hence wanted a ggplot solution! – biobudhan Oct 21 '21 at 18:50

score 2 · Accepted Answer · answered Oct 21 '21 at 17:12

This type of problems generally has to do with reshaping the data. The format should be the long format and the data is in wide format. See this post on how to reshape the data from wide to long format.

I will use the new pipe operator introduced in R 4.1.0.

library(ggplot2)

df1 |>
  tidyr::pivot_longer(G1:G3, names_to = "Group") |>
  ggplot(aes(Group, value)) +
  geom_boxplot()

Data

df1 <- read.table(text = "
           G1         G2       G3
S1  0.19021657  0.129541639 0.741696359
S2  0.431098317 0.791633452 0.502163442
S3  0.433107132 0.085196075 0.071400934
S4  0.800781053 0.221191986 0.918588422
", header = TRUE)

boxplot for single value containing data

2 Answers2

data

Data