Paste motif name to left of sequence logo and increase width of graph

zavolanlab / bindz-rbp

RBP module for bindz, a bioinformatics tool to detect regulators' binding sites on RNA sequences.

https://github.com/zavolanlab/bindz-rbp

Apache License 2.0

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Paste motif name to left of sequence logo and increase width of graph #36

Closed krish8484 closed 4 years ago

krish8484 commented 4 years ago

Description

Please include a summary of the change and which issue is fixed. Please also include relevant motivation and context. List any dependencies that are required for this change.

Addresses #34

Type of change

Please delete options that are not relevant.

[x] Bug fix (non-breaking change which fixes an issue)

Checklist:

[x] My code follows the style guidelines of this project
[x] I have performed a self-review of my own code
[x] I have commented my code, particularly in hard-to-understand areas
[x] My changes generate no new warnings
[x] I have added tests that prove my fix is effective or that my feature works
[x] New and existing unit tests pass locally with my changes
[x] I have not reduced the existing code coverage

krish8484 commented 4 years ago

Even after this PR, there is a limit of how much information one can show in a single PDF. The graph may still not look very pretty if the input sequence length increases to 200.

AngryMaciek commented 4 years ago

Why is that? what parts "will not be pretty?". For long sequences you can turn off the letter annotation of columns, as I mentioned in the issue, right? It is highly possible that in real life we will work with sequences of hundreds of letters.

krish8484 commented 4 years ago

Actually, its not bad, I ran the pipeline for an input sequence length of 300. This is the graph I got. One may have to use a good PDF viewer, so they can zoom in to view the graph clearly. For instance, opening it in Google Chrome will be good. ProbabilityVsSequence.pdf

AngryMaciek commented 4 years ago

Ok, this one is not bad, Let's make a test at maximum capacity - could you please run with a seq.len=1000 and full ATtRACT db and post the picture here as well?

AngryMaciek commented 4 years ago

The plot might look good but it is too heavy to parse by PDF viewers. As my system says - the image resolution is 18792 × 85248 - isn't that too much? You need to reduce the size of the file - currently me, a potential user, cannot even open it neither on mac nor Ubuntu. PTry to look into distinct formats, encoding etc. Maybe try raster image format, I am fine with raster in that case.

krish8484 commented 4 years ago

I tried plotting the graph in png, jpeg, tiff and svg png, jpeg and tiff returned an error due to image size (after googling about the error) Error in grDevices::png(..., res = dpi, units = "in") : unable to start device 'png'. Even after the scaling it down, using scale parameter, the jpeg image is not even close to good. svg file is too large, around 280 Mb

AngryMaciek commented 4 years ago

OK, let's leave it the way it is for now. It is OK for regular use-case. For a proper presentation of FULL ATtRACT database and very long sequences we will have to come up with another approach...