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chromoMap-An R package for Interactive visualization and mapping of human chromosomes

chromoMap-An R package for Interactive visualization and mapping of human chromosomes

by Lakshay Anand


Posted on May 18, 2018


chromoMap R visualization chromosome heatmap gene annotation Double-heatmap

vibrant, interactive, and informative chromosome plots created using chromoMap R package


Hello guys, This my very first post, on my own website, about an R package chromoMap that I have developed recently. (So forgive me for the mistakes if any )


What is chromoMap?

chromoMap is an R package that provides interactive, configurable and elegant graphics visualization of the human chromosomes allowing users to map chromosome elements (like genes, SNPs etc.) on the chromosome plot. It introduces a special plot viz. the "chromosome heatmap" that, in addition to mapping elements, can visualize the data associated with chromosome elements (like gene expression) in the form of heat colors which can be highly advantageous in the scientific interpretations and research work. Because of the enormous size of the chromosomes, it is impractical to visualize each element on the same plot. But chromoMap plots provide a magnified view for each of chromosome location to render additional information and visualization specific for that location. You can map thousands of genes and can view all mappings easily. Users can investigate the detailed information about the mappings (like gene names or total genes mapped on a location) or can view the magnified single or double stranded view of the chromosome at a location showing each mapped element in sequential order (You will see in the demos below). Not ony that, the plots can be saved as HTML documents that can be customized and shared easily. In addition, you can include them in R Markdown or in R Shiny applications.


How to Install It?

The very first release of the chromoMap (version 0.1) is available on CRAN ( The major repository for R packages). You can install it, like you'd install any other R package on CRAN:

install.packages("chromoMap")


For getting best visualizations and features, I would recommend using the RStudio.


Types of Chromosome Plots

There are three major categories of chromosome plots, that you can create using chromoMap:
( see the demo to view the interactive plots)

Annotation Plot

This is a basic chromosome plot that provide annotation of the elements(genes/SNPs) on the chromosomes with single color. On hovering over a location, Users can view the total number of elements mapped on that location along with their names in sequential order(in which they are mapped on the chromosome).


View Annotation Plot Demo


Heatmap-Single Plot

This plot is a chromosome heatmap that annotate the elements on the chromosome with heat colors (depend on the associated data for the element). The overall plot display an averaged heatmap i.e each location represent average data for all the elements in that location. On hovering over a location, users can view detailed heatmap for each element (almost like a magnified view for a location).A single strand is displayed with all elements placed on it in actual sequence and with actual heat color assigned to them.


View Heatmap-Single Plot Demo


Heatmap-Double Plot

his allows users to add secondary data for the elements. This plot display the heatmap with respect to the first data but also visualize the heatmap of secondary data (in magnified view) on a second strand placed in parallel for comparing the data of elements on same location. Hence, users can compare the element data in single plot.


View Heatmap-Double Plot Demo


Include chromoMap in your Web Applications!

chromoMap is actually an R HTML Widget that can easily be included in your R shiny web applications. To know about the chromoMap shiny API see the vignette. ( if you include chromoMap in your application, then let me know by contacting me, I will add the example references in this website for your project)


Save and share chromoMap plots as customizable HTML documents

You can easily save and share the plots you create as customizable HTML documents. You can add your project title and description in the HTML document and can share it as projects. Know more about this feature in the vignette.


How to use It?

I wrote a detailed vignette that include illustrative example codes and images. Please read the vignette for getting started with the chromoMap.


How to cite chromoMap?

There's a request. If you use chromoMap in your project, please use the citation:


Lakshay Anand (2018). chromoMap: Interactive Visualization and Mapping of Human Chromosomes. R package version 0.1.
https://CRAN.R-project.org/package=chromoMap



You can also create the general citation and the BibTex entry (for LaTex) in R using:


citation(package = "chromoMap")



Features Requests

I am actively developing this project and will be adding some new features in the next update for the package. This is the very first release of the package (version 0.1). If you have features you would like to have added or encountered a bug, please submit your suggestions and bug-reports by contacting me.





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Create chromosome heatmaps and annotate genes on chromosomes using chromoMap R package.


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