an error message - running the run.knetl

[MavroLucic]

Hi guys

I want to test the KNetL map for some geochemical purposes (sparse geochemical data 5600 rows and 19 columns). However, I have some problems, when I try to run the run.knetl, I get an error message.

#This is my code:

library(iCellR) my.obj <- make.obj(data)

Filtering the data my.obj <- cell.filter(my.obj) Normalizing the data my.obj <- norm.data(my.obj, norm.method = "ranked.glsf")

my.obj <- gene.stats(my.obj, which.data = "main.data")

Run PCA my.obj <- run.pca(my.obj, method = "base.mean.rank", data.type = "main") opt.pcs.plot(my.obj)

Run DR my.obj <- run.pc.tsne(my.obj, dims = 1:10, perplexity = 6) my.obj <- run.umap(my.obj, dims = 1:10) my.obj <- run.knetl(my.obj, dims = 1:10, zoom = 300, dim.redux = "umap")

#I got an error here

Getting PCA data Calculating euclidean distance ... Finding 300 neighboring cells per cell ... Generating graph from root to neighboring cells ... Generating 2D Layouts ... Error in dimnames(x) <- dn : length of 'dimnames' [1] not equal to array extent In addition: Warning messages: 1: In graph.data.frame(data, directed = FALSE) : In d' NA' elements were replaced with string "NA" 2: In get(layout.2d)(g) : Non-positive edge weight found, ignoring all weights during graph layout.

Can somebody help me?

Thank you in advance. Kind regards