Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • 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 Files
    Last edited by pirates.genome; 12-30-2013, 03:01 AM. Reason: added the input data

Latest Articles

Collapse

  • seqadmin
    Exploring the Dynamics of the Tumor Microenvironment
    by seqadmin




    The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...
    07-08-2024, 03:19 PM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, 07-25-2024, 06:46 AM
0 responses
9 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-24-2024, 11:09 AM
0 responses
26 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-19-2024, 07:20 AM
0 responses
160 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-16-2024, 05:49 AM
0 responses
127 views
0 likes
Last Post seqadmin  
Working...
X