I was wondering how to draw a venn diagram like pie chart in R, to show the distribution of my RNA-seq reads mapped onto different annotation regions (e.g. intergenic, intron, exons etc.). A google search returns several options, including the nice one... [Read more...]

I found this elegant note about reshape2 from Sean Anderson's blog:http://seananderson.ca/2013/10/19/reshape.htmlBasically,reshape2 is based around two key functions: melt and cast:melt takes wide-format data and melts it into long-format data.cast tak... [Read more...]

Google Doc is a good way to share/manage documents between you and your colleagues, but sometime you want to directly access the data in terminal (e.g. bash) or in program (e.g. R), without downloading the data first. For example, I have a Google Spre... [Read more...]

If it's an internal function of R (e.g. from base package), just type the function name, like__ rowMeansfunction (x, na.rm = FALSE, dims = 1L) {    if (is.data.frame(x))         x [Read more...]

I would like to recommend a recent workshop material on R/Bioconductor from Marc Carlson et al.http://www.bioconductor.org/help/course-materials/2013/SeattleMay2013/PDF: IntermediateSequenceAnalysis2013.pdfR script: IntermediateSequenceAnalysis201... [Read more...]

I got this Google Developers R Programming Video Lectures from Stephen's blog - Getting Genetics Done.Very useful R tutorial for beginner! Short and efficient. Here is what I learned after watching the lectures:4.3 - Add a Warning or Stop the Func... [Read more...]

Related papers to read:Model-based Analysis of ChIP-Seq (MACS)MACS can also be applied to differential binding between two conditions by treating one of the samples as the control. Since peaks from either sample are likely to be biologically meaningful... [Read more...]

Say I have a list of values, and I cut them by some break points, how do I know the number of values in each interval?We know cut() function in R works for the purpose.  For example,tx0 [Read more...]

I've drawn figure in R with lwd=1, e.g.pdf('test.pdf')plot(1:10, type='o', lwd=2, axes=F)box(lwd=1, col='red')dev.off()And then you open the PDF in Illustrator, you will see the border width is 0.75pt, and the line is 1.5pt, which seems that the unit ... [Read more...]

Did you notice that the file generated from write.table() in R has missed a tab (\t) in the top-left corner, when row.names=T (by default)?I found the solution here:http://stackoverflow.com/questions/2478352/write-table-in-r-screws-up-header-when-has-r... [Read more...]

Print publication usually ask to use CMYK (instead of RGB) color mode for figures (because not every color can be print out), while we usually use RGB for screen reading (because screen has larger range of color scale). Of course we can convert RGB to ... [Read more...]

We usually see NA and NaN in R. What's the difference between them?Here a good post for that topic:http://stats.stackexchange.com/questions/5686/what-is-the-difference-between-nan-and-naIn summary here:NaN ("Not a Number") means 0/0NA ("Not Available") is generally interpreted as a missing value and has various forms - NA_integer_, ... [Read more...]

Here is my working R code for the task. It can be simplified as 3 lines.# example of controling individual track#theURL="http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm9&wgRna=hide&cpgIslandExt=pack&ensGene=hide&mrna=hide&intronEst=hi... [Read more...]

This is my first SOM figure :)Thanks to the som package and example code from Jun Yan. Here is my code for the figure:require(som)rpkm [Read more...]

Motived by the post from FlowingData(http://flowingdata.com/2010/11/23/how-to-make-bubble-charts/), I made this plot with R code below:par(mfrow=c(3,1), mar=c(4,6,4,4))for(ty in c("protein_coding","lincRNA","piRNA")){          ... [Read more...]

I've not added tips for a while. Here is it for today:1. How to add title for graph with multiple plots?par(mfrow=c(1,2),oma = c(0, 0, 2, 0))plot(1:10,  main="Plot 1")plot(1:100,  main="Plot 2")mtext("Title for Two Plots", outer = TRUE, cex =... [Read more...]

From Wiki:"... the bottom and top of the box are always the 25th and 75th percentile (the lower and upper quartiles, respectively), and the band near the middle of the box is always the 50th percentile (the median). But th... [Read more...]

From Wiki:"... the bottom and top of the box are always the 25th and 75th percentile (the lower and upper quartiles, respectively), and the band near the middle of the box is always the 50th percentile (the median). But the ends of the whiskers can represent several possible alternative values..."... [Read more...]

Say you havea [Read more...]

Earlier I posted a blog for "k-means + heatmap" used for clustering analysis. Recently to prepare for the "Bioinformatics Tools" meeting, I made a slide with more details on "clustering analysis". Here it is:https://docs.google.com/presentation/d/1vMS3... [Read more...]