Question: How to generate a pie chart of genomic annotations of ChIP peaks
0
gravatar for cbio
2.9 years ago by
cbio400
cbio400 wrote:

I am interested in creating a Pie charts of ChIP-Seq reads corresponding to annotated regions of the hg19 genome.  I want to count the total number of peaks at given genomic locations were counted and standardize them to each region’s occupancy of the human genome (for example, promoters only account for ~0.8% of the human genome).

NOTE: I'm aware that pie charts are often looked down by this the bioinformatics community, so if anyone has another visualization option please feel free to let me know.

How would I go about generating this type of pie chart?

chip-seq • 1.5k views
ADD COMMENTlink modified 9 months ago by ATpoint10k • written 2.9 years ago by cbio400

Most of the time, a bar chart will do the job for you. Pie charts are considered a bad way of conveying information, see this article for reasons why. The first example is compelling enough to drop pie charts entirely. 

ADD REPLYlink written 2.9 years ago by h.mon21k
1
gravatar for vivekbhr
2.9 years ago by
vivekbhr510
Germany
vivekbhr510 wrote:

You can try HOMER to annotate the peaks then plot it the way you want, or if you work in R/bioconductor, try ChIPPeakAnno. It can give you both pie and bar charts.

ADD COMMENTlink written 2.9 years ago by vivekbhr510
0
gravatar for ATpoint
9 months ago by
ATpoint10k
Germany
ATpoint10k wrote:

You can use my script PieChart_annotatePeaksHomer.R. It reads the default output from HOMER annotatePeaks.pl, counts the number of peaks per genomic feature and plots a pie chart.

Pie Chart

ADD COMMENTlink modified 9 months ago • written 9 months ago by ATpoint10k
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