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saezlab / OmnipathR

R client for the OmniPath web service
https://r.omnipathdb.org/
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Omnipath database #73

Closed chrkuo closed 1 year ago

chrkuo commented 1 year ago

Hi I am trying to use omnipath as a reference database on NICHES.

I have a few question.

  1. How do i look at a list of the database of receptor ligand?

  2. is there a bug in the database because when i loaded it to run there are errors that keep popping up.

NICHES_output <- RunNICHES(object = EWS4512, LR.database = "omnipath", species = "human", assay = "alra", position.x = 'x', position.y = 'y', k = 4, cell_types = "seurat_clusters", min.cells.per.ident = 0, min.cells.per.gene = NULL, meta.data.to.map = names(EWS4512@meta.data), CellToCell = F,CellToSystem = F,SystemToCell = F, CellToCellSpatial = F,CellToNeighborhood = F,NeighborhoodToCell = T) 

                       Error:

**Set cell types as Identity of object internally

Subsetting to populations with greater than 0 cells

1437 distinct cells from 7 celltypes to be analyzed Error in mutate(): ℹ In argument: n_references = ifelse(...). Caused by error in map(): ℹ In index: 1. Caused by error in .f(): ! Arguments in ... must be passed by position, not name. ✖ Problematic argument: • outsep = outsep Run rlang::last_trace() to see where the error occurred.**

deeenes commented 1 year ago

Hello,

The issue that you're experiencing has been fixed long time ago (#57), you can update the package directly from git:

library(remotes)
remotes::install_github('saezlab/OmnipathR')

There are two kinds of ligand-receptor networks that you can retrieve from OmniPath: one is in silico constructed from many resources, it has high coverage, but lot of false positives, though you can do some quality filtering on it; and there are the literature curated ligand-receptor interactions. Please take a look at the documentation of the following functions, and if any of your questions remain unanswered, feel free to ask again: 1, 2, 3.