Cnv Visualisation

Question

[User 7572]

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

[Malachi Griffith]

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

[User 7572]

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

[User 7572]

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

Answer 1

[Damian Kao]

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.

[Chris Miller]

Agreed - looks like a custom R script to me.

[User 7572]

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,