Error in if (tolower(filter) == "novar") { : missing value where TRUE/FALSE needed

[Moonerss]

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 needed

I 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 needed

sessioninfo

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

[lstetson1]

I have the same issue. Were you able to resolve?

[watermelon1234567]

I have the same issue.

[OrangeBigBaby]

same problem

[tangmindan]

First, this bug appears on this step:

Second, errors began to appear in this conditional statement：

So，we can

   vis <- Vision(scaled_counts, signatures = gmtFile,meta=meta,cellsPerPartition=100)
    if(is.na(vis@params$latentSpace[["projectionGenes"]])){
        vis@params$latentSpace[["projectionGenes"]] <- vis@params$latentSpace$projectionGenesMethod
    }
   vis <- analyze(vis)