ClusterProfiler: Graphical output layout

[yvandenb]

Graphical display: layout to be improved (overlapping text, frame with reduced size, see below...) - Flo will discuss with Sam...

[combesf]

To be done (reminder) : to specify the "showCategory" parameter for the dotplot function for the clusterProfiler graphics

[combesf]

Done for the "showCategory" argument (committed on GitHub). Caution : set to 10 (categories to be showed). Would be better to be settable ?

[NguyenLien]

Updated on dev instance.

[yvandenb]

Thx Lien => will test

Would be better to be settable ? Ideally yes, this means that we have to define a range of categories: from 10 to X ?? what would be the max value according to what you've experienced ? Default value set at 10 should be OK to me...

[combesf]

let's 1st try with 10, and see ...

[yvandenb]

OK thx both of you, let's keep it like this for the moment...I propose to discuss this together along with the others enhancements posted related to 'ClusterProfiler', namely:

• Nbr of categories to be displayed (settable or not)
• In relationship with above, the layout of the dotPlot that is impacted (also on the x-axis that could be represented By geneRatio, Percentage or count)
• A new option allowing to upload your own background (by default currently : whole human reference proteome)

[yvandenb]

Meanwhile Lien, please could you

1. modify the .xml so that the input required by default option is "Input file containing your identifiers"
2. stilll in the .xml, in the user doc section parag "input required" replace "You can copy/paste these identifiers or supply a tabular file (.csv, .tsv, .txt, .tab) where there are contained." by "two modes are allowed: either by supplying a tabular file (.csv, .tsv, .txt, .tab) including your IDs (identifiers) or by copy/pasting your IDs (separated by a space).
3. once done deployed this version on dev and proteore.org...and let me know ;-) Thx

[yvandenb]

@Lien : did you deployed the updated version on proteore.org ?

[NguyenLien]

@yvandenb I've just updated the dev one. By the way, I'll do the same (default input option is from file) for all components.

[yvandenb]

:+1: Let me know once done...

[NguyenLien]

@yvandenb they are all updated now in dev and proteore.org.

[yvandenb]

As a reminder: graphical display and size-adjustment => layout to be improved (overlapping text, frame with reduced size, see below...) - Flo is on charge with Sam...

[yvandenb]

Flo regarde ce qu'elle peut ré-utiliser du code de Sam qui a ré-ecrit la fonction de display dot & bar-plot en utilisant ggplot2 et HighCharts

[yvandenb]

Display graphics à retester par Flo/Yves

[yvandenb]

Cela désormais OK sur cet aspect graphical layout - je ferme l'issue