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How to load local data file for a track #572
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This is not possible in the javascript libraries (including Gosling.js) by a security policy of browsers. You will need to have a server that serves your local data since the browser cannot access your local files directly. |
Can I ask how large the data is? Also, is the same data used multiple times in your specification? Would the use of a HiGlass server not be feasible in your case? |
There are about 1 million lines in the data file.
Yes, because there are multiple value columns in that file.
I'm trying to use a HiGlass server to solve this issue. However, it is a bit tricky because I created a synthetic genome which has only chromosome 1 by removing regions that are not covered by probes. The coverage data file of a sample in the bedgraph format was converted to a hitile file using the following command:
The data is for only about 350 genes, attached below: And then the hitile file was uploaded to the higlass server. By viewing the coverage data in browser I find the converted data looks something goes wrong , but I don't figure out what step goes wrong. @sehilyi A question about zoom levels: how can I know what the current zoom level is in gosling? Zhen |
@sehilyi I've already found the answer to this question in the source code for higlass: |
Sorry that my response was late but great to hear that you found the answer! Just curious -- since those are HiGlass code-bases, are you using those functions in your custom local Gosling.js on your machine? |
No, I've not used those functions yet, but just read the code. To other questions I still have not found answers. Is there a way to view the content of a hitile file just like the way to view a csv file? I want to make sure if hitile files that are created by us are in right form and meet our requirements. Zhen |
@zhangzhen Sorry for the late response. When I test your file (i.e., aggregate and ingest to the server), I see the following view, which seems to look fine for me. Could you elaborate on the issue you are confronting? Demo: http://higlass.io/l/?d=BOXopZfFS9-LTYLijCVekA Also, you would want to use a Since Hitile is based on HDF5, you can use HDF5 viewers, such as HDFView to browse metadata (e.g., chromosome sizes, assembly, ...) as well as raw values. |
I've put the tsv file RD2109054FFP.blockData.tsv into the public folder, and then set the data url in the spec as follows:
"url": "./RD2109054FFP.blockData.tsv"
Nothing is displayed in the corresponding track. To shorten the data loading time, I want to fetch the local file instead of the remote one. How can I do this?
Zhen
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