lgatto / 2017-spatialmap-robin

Robin's 'Spatial Proteomics Data Dissemination' project

• 📉️ Professor of Bioinformatics at the de Duve Institute, UCLouvain in Brussels, Belgium
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2017-spatialmap-robin's Issues

Features

A list of features that we might consider

• Features from the lab seminar (see issue #8)
• Peptide-level mapping: visualise observed peptides along the protein sequence (as isoforms). Not sure how to handle protein groups here.

MSnSet NA / Plot2D exception handler

While uploading all data to firebase (with the plot2D data in it) I got the following error:

Error in plot2D(eval(as.name(dName)), plot = FALSE) : 
  No rows left after removing NAs!

I then ran a lapply through the dataset and identified "havugimana2012" as the problematic MSnSet.
While we could add exeption handlers for that case, its rather problematic to add extra code for a single exeption, so I will exclude that dataset for now.

Dataset Page

In this issue we list all functionalities and ideas regarding the "Datasets" page on which all uploaded MSnSets can be found. Suggestions or screenshots of comparable websites and other ideas are welcome.

• Added all /meta entries
• Adding sorting/filtering system
• Adding search bar
• Enhance the display of the items
• Add private MSnSet entries to the query

Move discussions about UI

It's good to have the design issues, but they would probably be better in the repo that actually contains the page. Could you transfer the SpatialMapDev repo to the SpatialMap organisation and move these discussion there, please.

DataView Page

In this issue we list all functionalities and ideas regarding the "DataView" page, which displays among others the D3.js plot. Suggestions or screenshots of comparable websites and other ideas are welcome.

Plot Related:

• D3.js native plot integrated
• Toggle unknowns / text annoation
• Add profile plot
• Add D3.js point callback functionality (to make points clickable)
• Add/delete organelle coloring
• D3.js gradient coloring based on table value
• D3.js gradient scaling based on table value
• D3.js gradient transparency based on table value
• Toggle one/multiple plots

Table Related

• Table integrated
• Click on table entry highlights point
• Sort table on specific column
• Make column sizing flexible
• Add delete columns

API related:

• Add uniprot API (or other)

Other:

• Add metadata display
• Add point annotation
• Add save functionality

bottleneck: pRoloc::getMarkerClasses(object)

The extraction with getMarkerClasses takes 6+ seconds while generating only a short string, which might be soon a problem when we want to calculate the meta data on the slower shiny server for the uploading process.

I will look at the pRoloc method if we can get any performance improvement.

t-SNE evaluation

To set reasonable parameters for the t-SNE visualisation in the online app, we need to assess the hyper-paramters on all (or many) dataset. An example of how to do this is shown in the vignette. In a nutshell, one needs to iterate over a range of steps and perplexity values and produce the grid of PCA plots.

@Kohze - could you create an Rmd file with this analysis in sci-reports/rsne.Rmd and update this issue once it is ready. Thanks!

Lab seminar on Monday 5th June

@Kohze - you are up for a lab seminar on Monday 5 June. It would be good to have a mock of the whole website up and running, and a prototype of the data view page.

What we need to get out is as much constructive feedback as possible. To make that happen (as opposed to random opinions), we should ideally have a list of questions that we would like people to answer. I'll start the list below, please do amend as you see fit.

Design / Style

A page to collect the UI frameworks we can use and share screenshots of interesting references.

• currently used: http://dev.office.com/fabric#/components
• released this week: http://fluent.microsoft.com/

since the new fluent design is still close to the fabric components, we could re-create the new "fluent" design with all their features. Fluent design seems to be a mix of the apple minimalistic design and material design, which seems quite convincing.

Other react.js alternatives:

• Material UI: http://www.material-ui.com

More inspirations:

• https://site.uplabs.com/posts/c/resources/interface