Question

Is there a way to align Hi-C half heatmaps to Gviz track?

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Merienne Nicolas ▴ 120

@merienne-nicolas-6729

Last seen 7.0 years ago

Switzerland

Dear all,

I am trying to handle Hi-C data to represent interactions between DNA segments. I got the data from the ENCODE publication of Shen et al 2012, Nature, in which, for each chromosome, interactions are represented as a file containing the matrix of interaction. Considering that each bin represent 40kb in the chromosome, I could isolate rows and columns covering my sequence of interest and I used heatmap.2 to generate the 'half' heatmap of interactions. In parallele, I used the same coordinates to generate a Gviz track showing the genes present in the region as well as ChIP-Seq peaks. And finally, I am interested in merging the two figures together to visually determine which genes/epigenetic marks are in interacting domains. For the moment, I tried to do it manually but even if the size of both graphics should be the same, I can not precisely align the two figures. So, I am wondering if there could be a way to do it automatically?

Thank you very much.

Best,

Nicolas

Gviz Hi-C Heatmap • 2.0k views

ADD COMMENT • link updated 8.6 years ago by Nicolas Servant ▴ 260 • written 8.6 years ago by Merienne Nicolas ▴ 120

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Hi Nicolas,

Have you tried the plotting type "heatmap" for DataTrack ? Just for curiosity could you post a figure which you made manually and would like to create it in Gviz?

Best

Robert

ADD REPLY • link 8.6 years ago Robert Ivanek ▴ 750

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Hi Robert,

Actually, I did not try to do the heatmap with the DataTrack function. The data I am using are stored in an interaction matrix, in which each row/column represent a range of 40kb and each value represents the interaction intensity between the corresponding row and matrix. For example:

     V2000 V2001 V2002 V2003
2000     1     5     6     8
2001     5     4    22    28
2002     6    22     0    20
2003     8    28    20     9

In this subset, the 40kb range of the columnV2000 has '5' interactions with the 40kb range of the row2001. I noticed that the DataTrack function needs a GRanges or IRanges object and as I am beginners with Hi-C data, it was easier for me to make the heatmap with heatmap.2 rather than try to transform the matrix into a GRanges object.

I loaded one figure on Dropbox, the link is:

https://www.dropbox.com/s/xjqte2p5dodwxxp/TAD593.png?oref=e

Do not hesitate to tell me if the link is not working. As you can see, there is the Gviz plot with UCSC genes and ChIP-Seq peaks just under the half heatmap. It is feasible to do it manually, Gviz or any other tool would be interesting to automate the process (and will greatly reduce the time needed to generate all the plots...). But I don't know if DataTrack could be used to generate this kind of heatmap or if it could work with a matrix object.

Thank you for your help.

Best,

Nicolas

ADD REPLY • link 8.6 years ago Merienne Nicolas ▴ 120

score 0 · Answer 1 · 2016-04-19

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Nicolas Servant ▴ 260

@nicolas-servant-1466

Last seen 2.5 years ago

France

Hi Nicolas,

I would first advice you to have a look at the HiTC package which should help you handling such data. With HiTC, you should be able to plot your map and to add a track. However, the peaks will be interpreted as bars (i.e. start/end) below your maps ... so you will not have nice peaks. Otherwise, I would suggest to use other Hi-C tools to do that such as HiCPlotter for instance. Using HiTC, you can export your data in a HiCPlotter compatible format (see exportC function).

Hope it helps.

N

ADD COMMENT • link 8.6 years ago Nicolas Servant ▴ 260

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Hi Nicolas,

Thank you for your answer. Indeed, the package HiTC seems to be interesting to generate this kind of plots. I will test it and see how the peaks look like (if I can interpret my data, it could be ok for me).

Thanks.

Nico

ADD REPLY • link 8.6 years ago Merienne Nicolas ▴ 120