Box plot using ggplot2

Question

[1769mkc]

I can make box plot using the base R plot ,but I want to do the same with ggplot2 , its not as simple as making it in normal boxplot function ,

This is my data frame

 Gene     `7256_Mono` `7653_Mono` `6792_Mono` `6792_HSC` `7653_HSC` `7256_HSC`
 DNMT3A   9.8143600   5.5681400  3.32429000  7.7649600  7.8304600 21.9411000 
 DNMT3B   0.1053070   0.0826214  0.20910300  2.3988700  3.3696100  3.9184700

So this is my subset of data set how do I coerce this dataframe into ggplot data format , i have read tutorials but it quite confusing ,I have to make factors which is used in the ggplot , so how do i make factors out of this data sets so that I can use it for ggplot and make box plot out of it. Any help and suggestion would be highly appreciated .

[ddiez]

Take a look a tidy data, tidyverse and perhaps this older answer.

[ddiez]

Oh! I just noticed that you asked the question in the answer I mentioned! OK, here the solution will be similar I believe. If you have some trouble, try giving us the actual code you used (applied on the example data you provided).

[1769mkc]

okay I will use the same so i can use reshape the data to make it for the ggplot form i suppose i will give it a try first and lets see if I get the same or not

Answer 1

[willgilks]

Hi krushnach80, not sure how you want to group the variables, by but below is my solution.

> head(dat)
    Gene X.7256_Mono. X.7653_Mono. X.6792_Mono. X.6792_HSC. X.7653_HSC. X.7256_HSC.
1 DNMT3A     9.814360    5.5681400     3.324290     7.76496     7.83046    21.94110
2 DNMT3B     0.105307    0.0826214     0.209103     2.39887     3.36961     3.91847

## Libraries... I think there is one library for all these now.
library(tidyr)
library(dplyr)
library(ggplot2)

## Format the data as 'long' using dplyr %>% and tidyr gather, and omitting Gene. 
mdat = dat %>% gather(key = sample, value = val, -Gene)
head(mdat)
    Gene       sample       val
1 DNMT3A X.7256_Mono. 9.8143600
2 DNMT3B X.7256_Mono. 0.1053070
3 DNMT3A X.7653_Mono. 5.5681400
4 DNMT3B X.7653_Mono. 0.0826214
5 DNMT3A X.6792_Mono. 3.3242900
6 DNMT3B X.6792_Mono. 0.2091030

## Make boxplot with scatter overlay because boxplots can be misleading. Grouping factor is gene. Also try beeswarm-type plots.
ggplot(mdat, aes(Gene, val)) + geom_boxplot(colour = "grey", fill = "light grey") + theme_bw() + geom_jitter(width = 0.2, alpha = .9, shape = 2)