search

BioAnalyticResource / ePlant

ePlant is a gene-centric visualization tool for plant genomes
https://bioanalyticresource.github.io/ePlant/
GNU General Public License v2.0
7 stars 12 forks source link

eFP (tissue) views colouring and heat scale do not align with ePlant2 #144

Open VinLau opened 2 weeks ago

VinLau commented 2 weeks ago

The eFP views seem to have incorrect colouring where the colouring of tissues is based on the group maxima/minima versus the global (i.e. entire view) maxima values. This makes it such that the colouring is very different to (current) ePlant2.

To reproduce/see on ePlant2:

  1. Go to https://bar.utoronto.ca/eplant
  2. Enter a gene such as ABI3
  3. Go to the Tissue & Experiment Viewer
  4. Explore some views and look at their values, along the colour scale (see below):

image

Note the current view on ePlant in development for the same gene (ABI3):

image

Note that the value of '21.53' is the same on the tooltip however the colouring is vastly different. It should be closer to yellow than red as the maximum for the view is 120.64. Also the SD is slightly off.

The bottom-left heat scale is off.

We will need to refactor how the getColor function (svg.tsx) works and/or potentially how to parses the XML to include global maximum.

VinLau commented 2 weeks ago

I can use the min/max (need to refactor?) inside getInitialData inside index.tsx of EFP (https://github.com/BioAnalyticResource/ePlant/blob/2ff7e04e16499c38e790d8f0cbdca6aa29608b93/Eplant/views/eFP/index.tsx#L167) to grab the view-global maximum for colouring.