using iSEE explorer to visualize objects generated by

[tobiasko]

Hi maintainers,

nice idea to use std. Bioc containers to work with proteomics data! My main interest is currently web-based visualisation/exploration through tools like iSEE. With this in mind i tried the following code:

setwd("~/Downloads/2347343")
sceL <- einprot::importExperiment(inFile = "combined_protein.tsv", iColPattern = "\\.MaxLFQ\\.Intensity$")
> sceL
$sce
class: SingleCellExperiment 
dim: 371 6 
metadata(1): colList
assays(9): MaxLFQ.intensity Unique.spectral.count ... MaxLFQ.total.intensity Intensity
rownames(371): 1 2 ... 370 371
rowData names(16): Protein Protein.ID ... Combined.Total.Spectral.Count Indistinguishable.Proteins
colnames(6): X20230815_C32568_002_S547392_KO1_Control X20230815_C32568_003_S547397_17.2_WT ...
  X20230815_C32568_007_S547393_KO2_Control X20230815_C32568_008_S547394_16.1_Mutant_rep
colData names(0):
reducedDimNames(0):
mainExpName: NULL
altExpNames(0):

$aName
[1] "MaxLFQ.intensity"

which gave me a valid single cell experiment container, but I fail to visualise it using the std. way to run the iSEE shiny app:

> app <- iSEE(sceL)
The `name` provided ('') does not correspond to a known icon
The `name` provided ('') does not correspond to a known icon
The `name` provided ('') does not correspond to a known icon
The `name` provided ('') does not correspond to a known icon
The `name` provided ('') does not correspond to a known icon
The `name` provided ('') does not correspond to a known icon
The `name` provided ('') does not correspond to a known icon
The `name` provided ('') does not correspond to a known icon
The `name` provided ('') does not correspond to a known icon
> shiny::runApp(app, launch.browser = TRUE)

Listening on http://127.0.0.1:3869
Warning: Error in <Anonymous>: unable to find an inherited method for function ‘cleanDataset’ for signature ‘"list"’
  44: stop
  43: <Anonymous>
  42: iSEE::cleanDataset
  41: eval [<text>#1]
  40: eval
  39: .initialize_server
  38: server
   1: shiny::runApp
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘cleanDataset’ for signature ‘"list"’

Is this due to missing metadata? Your R script launches iSEE after statistical testing has been performed, but for exploration is would be nice to look at the "raw" quantification results prior to testing. Possible?

[csoneson]

Hi @tobiasko - thanks for your interest! Note that your sceL object is a list containing both the SCE object and the name of the main assay - you need to pass sceL$sce (the SCE object) to iSEE.

[tobiasko]

uuups...capital fail! ok, now it runs. THX! I never worked with the SummarizedExperiment class before, but one could have guest by the name that it is a list.

[csoneson]

Cool 🙂 I'll close this issue then, feel free to open a new one if you have other questions or run into problems.