An easy to convert list to long table
Say you have a list with different lengths of vectors, e.g. __ head(genesets_list)$KEGG_GLYCOLYSIS_GLUCONEOGENESIS [1] "ACSS2" "GCK" "PGK2" "PGK1" "PDHB" "PDHA1" "PDHA... [Read more...]
Articles by Xianjun Dong
A bug related to R factor
Note a bug in my code today. Sometimes you need to put a certain level (e.g. healthy control) in the first position for your covariance. Here is my old code:dds[[variable]]=factor(dds[[variable]])levels(dds[[variable]])= union(variable_REF, levels... [Read more...]
Note (2) for DESeq2 time series data analysis
More notes on using LRT to test time-series data. Thanks for the discussion with Jie. swapping the levels of time factor won't change the LRT results, as if the time variable is a factor, LRT won't see it as a trajectory analysis but rather a fact... [Read more...]
Note for DEseq2 time course analysis
In many cases, we need to perform differential expression across the time course data, e.g. finding genes that react in a condition-specific manner over time, compared to a set of baseline samples. DEseq2 has such an implementation for time-course expe... [Read more...]
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/
PCA plot with fill, color, and shape all together
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 ... [Read more...]
Download all KEGG pathway KGML files for SPIA analysis
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... [Read more...]
Best way to draw heatmap for publication
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 ... [Read more...]
Best way to draw heatmap for publication
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... [Read more...]
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. ...
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...
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... [Read more...]
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 ... [Read more...]
My note on multiple testing
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 ... [Read more...]
My note on multiple testing
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 ... [Read more...]
How to correctly set color in the image() function?
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,... [Read more...]
Tips and Tools you may need for working on BIG data
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... [Read more...]
X11 connection error in Mac
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 ... [Read more...]
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 ... [Read more...]
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... [Read more...]
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