Thanks for this awesome package.
When I use it with a dataset contain about 190,000 cells，I got an error：
Error in if (tolower(filter) == "novar") { : missing value where TRUE/FALSE neededI think it maybe caused by the judgment condition not matching the condition content when run applyMicroClustering in poolCells.
## code in poolCells
if (is.null(object@params$latentSpace[["projectionGenes"]])){
filterInput <- object@params$latentSpace$projectionGenesMethod
} else {
filterInput <- object@params$latentSpace$projectionGenes
}
if (length(object@Pools) == 0) {
pools <- applyMicroClustering(
object@exprData,
cellsPerPartition = object@params$micropooling$cellsPerPartition,
filterInput = filterInput,
filterThreshold = object@params$latentSpace$threshold,
latentSpace = object@LatentSpace,
K = object@params$numNeighbors)
object@Pools <- pools
}Below is the code I run：
> vis <- Vision(cpm_mat, signatures = pathway_gmt, meta = cpm_seurat@meta.data)
Loading data from /public/home/ezhao/qian_lab/raw_data/myself/analysis/metabolism/data/raw_data/latest_main_metabolism_pathway.gmt ...
Using 17620/17638 genes detected in 0.10% of cells for signature analysis.
See the `sig_gene_threshold` input to change this behavior.
Over 100000 input cells detected. Enabling micropooling with max 10 cells per pool.
> vis <- analyze(vis)
Beginning Analysis
Performing micro-pooling on 185621 cells with a target pool size of 10
Computing a latent space for microclustering using PCA...
Determining lateng space genes...
Error in if (tolower(filter) == "novar") { :
missing value where TRUE/FALSE neededsessioninfo
R version 4.3.2 (2023-10-31)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS/LAPACK: /public/home/ezhao/software/base_use_conda/lib/libopenblasp-r0.3.25.so; LAPACK version 3.11.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
time zone: Asia/Shanghai
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] AUCell_1.24.0 fgsea_1.28.0 Seurat_5.0.1 SeuratObject_5.0.0
[5] sp_2.1-2 lubridate_1.9.3 forcats_1.0.0 stringr_1.5.1
[9] dplyr_1.1.4 purrr_1.0.2 readr_2.1.4 tidyr_1.3.1
[13] tibble_3.2.1 ggplot2_3.5.0 tidyverse_2.0.0 VISION_3.0.2
Thanks for this awesome package.
When I use it with a dataset contain about 190,000 cells，I got an error：
I think it maybe caused by the judgment condition not matching the condition content when run
applyMicroClusteringinpoolCells.Below is the code I run：
sessioninfo