SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Genomic data plotting/visualization pirates.genome Bioinformatics 2 05-15-2014 10:56 PM
Genomic coordinates to gene names Layla Bioinformatics 8 04-17-2014 03:23 PM
Converting contig coordinates to genomic coordinates aurimas Bioinformatics 0 03-06-2013 12:06 PM
Obtaining UCSC Genomic sequence Given Genomic Coordinates modi2020 Bioinformatics 0 12-03-2012 08:45 PM
Genomic coordinates from Gene Names Palgrave Bioinformatics 0 05-09-2012 03:40 AM

Reply
 
Thread Tools
Old 12-30-2013, 01:30 AM   #1
pirates.genome
Member
 
Location: Earth

Join Date: Mar 2012
Posts: 11
Question visualization of CNV with genomic coordinates in R ggplot2 or ggbio

Hi all,

I came through a heatmap of CNVs from Illumina Genome Studio which has four samples (see attachment). On Y axis they have genomic coordinates and on X axis the samples. Red denotes amplification and blue denotes deletion. I was wondering how can we make similar heatmap in R for CNV data or expression data? I know a little basis of ggplot and ggbio but I don't know how to make heatmap with genomic coordinates on Y axis.
CNV data is in segments:

chr start end copy-number
chr1 23432 25925 4
chr2 1375364 1378364 1

etc....

Thanks in advance.
Attached Images
File Type: jpg CNV heatmap.jpg (31.1 KB, 34 views)

Last edited by pirates.genome; 12-30-2013 at 03:01 AM. Reason: added the input data
pirates.genome is offline   Reply With Quote
Reply

Tags
cnv, ggbio, ggplot, heatmap

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 12:09 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO