R

R programming language

Identifying a point in ggplot2

So you have spent much time converting your simple R plot to a full-fledged ggplot2 graph with all its bells and whistles just to find that you are unable to identify a point on this graph to further investigate it. Indeed, the typical identify method is not applicable to ggplot2 graphs. Fortunately, there is a solution, which involves performing all the work yourself by going under the hood of ggplot2 to access the low-level graphics system on which it is [...]

By | March 11, 2015|Categories: Bioinformatics, Data Visualisation, R|0 Comments

Table-reading: loading data into R without a hassle

The first thing I have learned in R is how to load a table. Usually, when you start your R journey, someone more knowledgeable will tell you how to do this very first action. It will typically be: data<-read.table("~/SomeFolder/datafile.txt") You probably will be adding various parameters into the brackets such as "row.names=0" or "header=TRUE" or, "sep="\t"", to make sure you are reading your file correctly. And this is perfectly fine, as a loading method of small datasets. However, to maximize [...]

By | February 5, 2015|Categories: Bioinformatics, Biology, Performance, R|1 Comment

One task, three ways

Usually, there is more than one way to accomplish a task. Some are better, some are worse and others are just as good. Assessing which one to use is often related to the computing time, the ease of use and/or to personal preferences and abilities. Say I have a matrix of thousands of chromosomal features with the following column names : Feature, Start, End. All the positions are found on the same chromosome and the widths of my features are variable. [...]

By | January 15, 2015|Categories: Bioinformatics, R|0 Comments

Teach me how to box-plot!

Boxplots are everywhere! Publishers like boxplots.  But ask some people and most don't even know what a boxplot represents!  Recently I wanted to examine gene expression data between two samples for a certain gene. The gold standard to look at it would be *drum roll*... A boxplot! Interesting fact #1: Did you know a boxplot is called a “box and whiskers plot” as well?  Let's take a look! A boxplot is easily generated in the analysis software R and its interpretation [...]

By | September 21, 2014|Categories: Data Visualisation, R, Statistics|0 Comments

RStudio and version control

A version control is just a way to keep track of changes made to files throughout time.  It allows you to return to previous versions later.  I bet you are already using one without even knowing it! When you copy a file or a script before modifying it, you're using version control.  However, your manual version control may become hard to deal with at some point.  That's why it's worth investing time early on in a project and use a [...]

By | June 10, 2014|Categories: R, Version Control|Tags: , |0 Comments