Loading in a dataset in a custom format

[pakiessling]

Hi again,

I am trying to load in our Merfish dataset and I am running into a few problems with formVoltRon.

I have

• a dgTMatrix in gene x cell orientation
• a metadata data frame
• a coordinate data frame

I always get the error "Entity IDs are not matching" when I run

vr_object<- formVoltRon(data = matrix,
                        metadata = metadata,
                        coords = coordinates,
                        main.assay = "Merfish",
                        assay.type = "cell",
                        sample_name = "sample1")

All files have the same length and the same rownames.

Any ideas?

[Artur-man]

Hmm, that is unexpected. My test data with coordinates, metadata and matrix having the same dimensions and rownames perform well but I am currently testing other possibilities that may have cause this.

Will let you know ... meanwhile I made the following changes

• vrAssay objects to support both matrix and dgCMatrix
• check for cases that coordinate data introduced as a data.frame rather than matrix

Artür

[Artur-man]

@pakiessling Perhaps it might also help me if I get a look at the formatting of the rownames and cell IDs. Can you do a head() on rownames (or colnames in gene x cell matrix) and post it here ?

[pakiessling]

Ah it works now on the latest version from your repo - disregard

[Artur-man]

Ah no worries :) thanks a lot for the feedback <3