I've posted an updated and expanded version of this page: pch and colors in R.  Even though this is four years old it is one of my most popular posts so I felt it deserved better treatment than I had given it in the past.

cheers

Heath

It seems that at least every couple of weeks I need to make a graph in R that involves using different symbols on the same plot.  It’s not too hard to find a guide to the values for the pch parameter a quick google image search usually works fine.  However, it’s pretty straight forward to make a graph that shows them as well.  Here is the code that you need to run.  I borrowed a bit of the code from: http://gallery.r-enthusiasts.com/sources/source_157.R

plot(c(0,4.5),c(0,4),main="pch=",xaxt="n",yaxt="n",cex.main=2.5, col="white")
for (i in 0:24) {
  points(i %% 5, i %/% 5, pch=i,cex=2)
  text(0.3+ i %% 5, i %/% 5, i, cex=2)
}

And the result is:
Cheers

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This semester I am teaching an experimental design course.  However, three of my learning goals for my students are more general than experimental design:

  • munge a big dataset into different formats
  • use R to visualize their data and explore possible relationships
  • create scripts in R that process data do statistical test and output final plots for manuscripts

I wanted to justify the importance of learning good coding, scripting, computational skills to my students so I decided to mine the Evoldir mailing list for the last month or so.  I first downloaded all of the adds for postdoc positions that were posted from December 1, 2017 to January 15, 2018.  There were a total of 86 adds.  For each one of these adds, I first determined whether any computational skills were listed as desired/required for applicants.  Next, I counted the occurrence of requests for several more specific skills like knowing specific languages.


What I found was that 74% of the adds listed some form of computational skill as desired or necessary in the applicant.  The bioinformatics category included all adds with vague statements like "competitive applicants will have experience running bioinformatic analyses of..."  The misc. languages category included versions of C, awk,  and java.

I should note that in some ways my approach underestimates the importance of computational skills.  For instance, several of the adds that listed no computational skills are for departmentally funded independent postdocs.  These advertisements usually list no skill requirements despite the fact that many departments and selection committees will none the less rate these skills as important in reviewing an applicants plans or previous contributions.  The asterisks do not indicate anything about the add.  Rather, these are skills that my students should begin developing in my class this semester if they work hard.

So the answer is yes. Having computational skills will almost always increase your productivity and this is becoming more and more widely appreciated.

* On a sad note more adds listed knowing Perl as a desired trait than unix or modeling - ugh!




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I am broadly interested in the application and development of comparative methods to better understand genome evolution at all scales from nucleotides to chromosomes.
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