Blog Archives

Making Art in R

October 15, 2018
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Making Art in R

Amazing artworks people made in R:See their source code and more arts at:http://www.r-graph-gallery.com/286-antonio-sanchez-dataart/

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PCA plot with fill, color, and shape all together

September 25, 2018
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When I plotted the PCA results (e.g. scatter plot for PC1 and PC2) and was about to annotate the dataset with different covariates (e.g. gender, diagnosis, and ethic group), I noticed that it's not straightforward to annotate __2 covariates at the same time using ggplot. Here is what works for me in ggplot:pcaData

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Download all KEGG pathway KGML files for SPIA analysis

June 8, 2018
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Most people know KEGG pathway, but not everyone knows that it costs at least $2000 to subscribe its database. If you want to save the cost a bit, you can manually download the KEGG pathway KGML files and install in SPIA. Here I have a workaround to dow...

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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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Best way to draw heatmap for publication

July 8, 2016
By

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, so that you can kill your Illustrator; (ii) annoying grey boxes added...

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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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My 15 practical tips for a bioinformatician

February 16, 2016
By
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 you run tools with random option, e.g. bedtools shuffle, random etc.; You (or your boss in a day)...

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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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Calculate the odd of winning Powerball in R

January 12, 2016
By
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...

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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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