Welcome to the Visual World... 

ChromoViz is an R package for multimodal visualization of microarray data, 
DNA copy number alterations, cross-platform and cross-species comparisons, 
and genomic non-expression data obtained from public databases onto chromosomes.

ChromoViz: Multimodal visualization of gene expression profile onto chromosomes using Scalable Vector Graphics. 

Jihoon Kim, Hee-Joon Chung, Chan Hee Park, Woong Yang Park, Ju Han Kim 
Bioinformatics 2004;20:1191-1192 

Demonstration: Example Output
Software: ChromoViz_1.1.tar.gz (Linux)
software: (Windows)
Dataset : sampleInput.txt
Contact : Jihoon Kim

Tested on Linux and MS-Windows 2000/XP platforms.

Example code in R:

data( exprStemcell)
cViz( exprStemcell, humanBand, refSp="human")

fList <- c( "sampleInput.txt" )
featureSet <- cViz.loadFiles(fList)
cViz(featureSet, humanBnad, refSp="human")

Input to ChromoViz 

One needs to create CVF (Chromosomal Visualization Format) file as an input to ChromoViz. 
A CVF file can be easily created by entering accession- number, expression- level 
(i.e., <id>, <value>) pairs to the following form.

Track name:

Enter your list of <id>-<value> pairs, tab-delimited.

.. or you can upload your tab-dilimited text file:

An example input-format:
NM_020299          4.3 
NM_003718          5.5  
NM_004874          11.1 
NM_020647          23.4 
NM_005271          0.0 

The GRIP (Genome Research Informatics Pipeline) integrates major databases to resolve the position
and strand information from the input accesion numbers. GRIP integrates NCBI's GenBank, UniGene,
LocusLink, RefSeq, Homologene, UCSC Golden Path's refGene, knownGene, all_mRNA, all_est, 
NetAffyx ( and NCBI's report for chromosome and 
cytogenetic band ( maps/mapview/).

One can freely append non-expression data with user-defined position and value information 
as an additional track to the input CVF file using plain text editors for ChromoViz visualization. 
As a matter of fact, GRIP cannot resolve the information without accession numbers.

Enjoy visualizing with SVG viewer plug in to your web browser.

Powered by SNUBI