Blog Archives

Best way to draw heatmap for publication

July 8, 2016
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Here are two tips I can share if you were also working on a big dataset towards a high quality heatmap:1. Don't generate PDF using pheatmap() or heatmap.2() as (i) the file is unnecessarily SUPER large if you have a lot of data points in the heatmap, s...

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My 15 practical tips for a bioinformatician

February 16, 2016
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My 15 practical tips for a bioinformatician

Tips below are based on the lessons I learnt from making mistakes during my years of research. It's purely personal opinion. Order doesn't mean anything. If you think I should include something else, please comment below.Always set a seed number when y...

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Calculate the odd of winning Powerball in R

January 12, 2016
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Calculate the odd of winning Powerball in R

This Wednesday’s Powerball grand prize already climbed up to $1.5 BILLION. If you choose to cash out, it would be $930 million. And it keeps increasing…So, what’s the odd of winning the jackpot prize?Here is the game rule according to Powerball.com:…we draw five white balls out of a drum with 69 balls and one red ball out of a...

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My note on multiple testing

December 4, 2015
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It's not a shame to put a note on something (probably) everyone knows and you thought you know but actually you are not 100% sure. Multiple testing is such a piece in my knowledge map.Some terms first:- Type I error (false positive) and Type II error (false negative): When we do a hypothesis test, we can categorize the result into...

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How to correctly set color in the image() function?

May 15, 2015
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Sometimes we want to make our own heatmap using image() function. I recently found it's tricky to set the color option there, as its manual has very little information on col:cola list of colors such as that generated by rainbow, heat.colors,...

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Tips and Tools you may need for working on BIG data

May 8, 2015
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Nowadays everyone is talking about big data. As a genomic scientist, I could feel hungry of a collection of tools more specialized for the mediate-to-big data we deal everyday.Here are some tips I found useful when getting, processing or visualizing la...

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X11 connection error in Mac

March 11, 2015
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Typically, I log into my remote server/cluster via "ssh -X" and from there launch R program for plotting. But it always shows an error asunable to open connection to X11 display ''after a while, when you want to call functions such as plot(). This is very annoying. So that I have to exit the server and re-login again. Does this sound...

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reshape: from long to wide format

February 26, 2015
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reshape: from long to wide format

This is to continue on the topic of using the melt/cast functions in reshape to convert between long and wide format of data frame. Here is the example I found helpful in generating covariate table required for PEER (or Matrix_eQTL) analysis:Here ...

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vennpieR: combination of venn diagram and pie chart in R

September 25, 2014
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vennpieR: combination of venn diagram and pie chart in R

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 from Xiaopeng's bam2x (see below). However, he told me it's not released yet. And it's javascript...

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How to draw venn pie-agram (multi-layer pie chart) in R?

September 25, 2014
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How to draw venn pie-agram (multi-layer pie chart) in R?

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...

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