How To Create A Barplot In R That Shows Distribution Of Amino Acid Changes In Somatic Mutation.

Question

[shilpy]

Using R, how to create a barplot showing distribution of amino acid changes in somatic mutation.

[Obi Griffith]

Do you already have the list of amino acid changes tabulated? If so, then this isn't really a bioinformatics question as much as a question of how to use R at a very basic level. I suggest you try one of the many good online tutorials on how to use R like this one or maybe sign up for an R course like this one.

Answer 1

[Manu Prestat]

I like dotchart() for achieving that task. Take a look in seqinr cookbook:

• p60: what you want to do
• p87: codon usage example
• p107: amido acids factorial correspondence analysis coordinates

By the way, I don't know why dot charts are less popular than bar charts, these are most of the time clearer. In addition, if you have several classes to compare, it avoids stacked bar charts which, to me, are unreadable.

[Daniel]

That is the weirdest intro to a package I have ever read...

[Manu Prestat]

I'm surprised: the intro only! He can also publish his kid's drawing to teach genomic landscape ;-) http://www2.unil.ch/comparativegenometrics/049906.pdf

Answer 2

[Giovanni M Dall'Olio]

Just import the table containing your data, and use the barplot function to generate the plot.