Dot Plot for a matrix

Question

[dktarathym]

I have a matrix.

Dimensions=> rows= 6534, columns= 6

rows are the ORF (yeast)

columns are the name of the vcf files of yeast.

This matrix stores the information of no. of mutations occurring for a particular gene in each file (0 means, there is no mutation of that particular gene in the file)

> head(matrix)
          D784G    DAS217    dst1    E1224G    F1205H    rpa12
Q0010     0        0         0       0         0         4
Q0032     0        0         0       0         0         0
Q0055     1        1         1       1         1         1
Q0075     0        0         0       0         0         0
Q0080     0        0         0       0         0         0
Q0085    15        12        13      10        13        15

I want to make a dot plot:

X-axis= genes, Y-axis= No. of mutations for all 6 files in 6 different colors & shapes. Also, there should be a legend for the 6 files.

I am confused. How to write command for this?

Regards,
Deepak

Answer 1

[Devon Ryan]

1. Use the reshape2 package to convert that matrix to a format with the following columns: Gene (these will repeat once per sample), number of mutations, and sample.
2. Use ggplot to make the dot plot. If you set colour= to the sample column then it'll generate the legend for you.

[dktarathym]

Thank you Devon

Answer 2

[komal.rathi]

This is a very direct question to get others to do your homework but I am assuming you have absolutely no background in R because I see no code showing that you at least tried. From hereon, you should work on your R skills. Meanwhile you can use this code:

library(ggplot2)
library(reshape2)

# use melt function to transform your dataset for ggplot2
# it melts your dataset such that first column contains genes, second column has sample names and third column has the mutation value
dat = melt(matrix)
head(dat)

   Var1  Var2 value
1 Q0010 D784G     0
2 Q0032 D784G     0
3 Q0055 D784G     1
4 Q0075 D784G     0
5 Q0080 D784G     0
6 Q0081 D784G    15

# create plot using ggplot function. geom_point() is used for creating dot plots
ggplot(data = dat,aes(x = Var1, y = value)) + 
  geom_point(data = dat,aes(pch = factor(Var2), colour = factor(Var2))) + 
  xlab('Genes') + scale_shape_discrete(name="LegendTitle") + scale_colour_discrete(name="LegendTitle")

Play with the ggplot2 package to understand what each function is doing.

[dktarathym]

Thank you Komal for the help. This was a direct question, as I want to make it understandable, what I want. Therefore, I didn't showed any coding. And I am new to Biostars and using R from last few months only.

I did tried with ggplot2 package, but didn't knew about the reshape2 package. Thank you.