How to plot a graph with ggplot

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I have the following data.frame: 

                     sample OPN1SW  OPN1MW OPN1LW    RHO   OPN3   OPN4   OPN5
1: GTEX-11WQK-1026-SM-5EQLX  2.365  0.0000      0  4.138 86.322 40.199 12.533
2:  GTEX-XQ3S-1426-SM-4BOPR 22.317  0.0000      0 30.693 84.376 33.564  0.000
3:  GTEX-WHPG-2626-SM-3NMBR 21.142  0.6874      0 29.372 89.879 48.453  0.000
4:  GTEX-WEY5-2326-SM-3GIKK  0.000 16.2860      0 28.632 83.683 23.741  0.000
5: GTEX-14A5H-0826-SM-5QGPJ 20.448  0.0000      0 28.585 80.831 44.142 13.579
6: GTEX-132AR-0326-SM-5KM2C 12.052  0.0000      0 26.375 78.887 29.123 12.052

Full Data: link

It is a small sample of a database of the Xena Browser (Bioinfo); Columns are the generic expression, while the rows are the samples.

I need to make a graph of boxplot , where the generic expression is the x axis and the values are y

The problem is that I can not do this, I tried the following way: 

qplot(OPN1SW,sample,data = sk, geom='boxplot')

However,itisnotwhatIneed;WhatIneedissomethinglikethis:

X-axis names would be the samples of my table. I guess I'm missing X and Y at the time of plotting, but I do not know how to solve this, because each column must be boxplot with the appropriate calculated values. How can I solve this? Thanks for the help.

    
asked by anonymous 31.12.2017 / 15:52

1 answer

3

Your problem is in the organization of the data frame sk . ggplot2 is a very demanding package with the form of the data to be plotted. Ideally, one column has all the values of the gene expression and another column has all the names of the genes.

A practical way to organize the data is through the command melt of the reshape2 package: 

library(reshape2)

sk_melt <- melt(sk)

Note that the data frame sk_melt has 3 columns:

  • sample : self-explanatory

  • variable : with the names of the genes in the original dataset

  • value : with the values of the gene expressions associated with each gene, in each sample

Now just do the boxplot with the new data set sk_melt . I particularly do not like qplot . I think the chart gets more organized using ggplot in length. So, use the following commands and your chart will be ready: 

library(ggplot2)

ggplot(sk_melt, aes(x=variable, y=value)) +
  geom_boxplot() +
  labs(x="Gene", y="Expressão Gênica")

    
31.12.2017 / 18:16
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