Question: Cnv Visualisation
0
gravatar for User 7572
8.5 years ago by
User 75720
User 75720 wrote:

Dear All, I need to visualize my CNV data in the same way as it in this page. Could you please help me out???

http://www.biomedcentral.com/1471-2164/12/414/figure/F1

Input format is something like this:

Chr StPos EndPos sizeofCnv(kb) CNV(loss/gain) SDoverlap(0/1)

Thanks a lot

visualization cnv • 1.9k views
ADD COMMENTlink modified 8.4 years ago by Damian Kao15k • written 8.5 years ago by User 75720

If you post an example data file you might get a response that includes some R code and example output...

ADD REPLYlink written 8.5 years ago by Malachi Griffith18k

Dear Malachig, My input file looks like this...

Chr StPos EndPos Bins CN SD

10 1 1000 1 0 0 10 1001 2000 1 4 1 10 2001 3000 1 4 1 10 3001 4000 1 4 1 10 4001 5000 1 4 1 10 5001 6000 1 1 0 10 6001 7000 1 2 0 10 7001 8000 1 10 0 10 8001 9000 1 2 0 10 9001 10000 1 2 0 10 10001 11000 1 2 0 10 11001 12000 1 2 0 Thanks a lot

ADD REPLYlink written 8.5 years ago by User 75720

each line will be after each other not like the one displayed here. Sorry

ADD REPLYlink written 8.5 years ago by User 75720
3
gravatar for Damian Kao
8.5 years ago by
Damian Kao15k
USA
Damian Kao15k wrote:

It looks like they might have just generated a horizontal stacked bar graph. Each stacked segment can be defined with your raw data. So a CNV segment will just be another bar in the same stack.

You can probably use R to generate something similar. You'll have to write some scripts to transform your data into a format suitable for R.

Personally, I like using [?]ggplot2[?] to generated my graphs.

ADD COMMENTlink written 8.5 years ago by Damian Kao15k

Agreed - looks like a custom R script to me.

ADD REPLYlink written 8.5 years ago by Chris Miller21k

I am new to R so could you please suggest me a way so that I can try myself? My data is in this format:

Chr StPos EndPos Bins CN SD

Thanks a lot,

ADD REPLYlink written 8.5 years ago by User 75720
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