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wu-yc / scMetabolism

Quantifying metabolism activity at the single-cell resolution
BSD 3-Clause "New" or "Revised" License
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Error in sc.metabolism.Seurat #12

Closed longLabzj closed 1 year ago

longLabzj commented 2 years ago

Hello, when i did the first step to input my Seurat to quantify single-cell metabolism,it has problem as follow: `> countexp.Seurat<-sc.metabolism.Seurat(obj =immune, method = "VISION", imputation = F, ncores = 1, metabolism.type = "KEGG")

Your choice is: KEGG Start quantify the metabolism activity... Loading data from C:/Program Files/R/R-4.0.2/library/scMetabolism/data/KEGG_metabolism_nc.gmt ...

Using 20447/30242 genes detected in 0.10% of cells for signature analysis. See the sig_gene_threshold input to change this behavior.

Beginning Analysis

Computing a latent space for expression data...

Determining projection genes... Applying Threshold filter...removing genes detected in less than 2364 cells Genes Retained: 8259 Applying Fano filter...removing genes with Fano < 2.0 MAD in each of 30 bins Genes Retained: 1781

Clustering cells... Using latent space to cluster cells... Error in igraph::cluster_louvain(g) : REAL() can only be applied to a 'numeric', not a 'builtin' In addition: Warning message: In readSignaturesInput(signatures) : NAs introduced by coercion`

Firstly, i doubed that it was something wrong about my Seurat object. However, it had the same problem when i run the example "pbmc_demo.rda", how could i do to fix it? So many thanks!!

wu-yc commented 1 year ago

Please re install the vision v2.1.0. devtools::install_github("YosefLab/VISION@v2.1.0")