spatialLIBD
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Published
20 hours ago •
LieberInstitute
LieberInstitute
[BUG] Error during extract and reformat enrichment results when using `registration_wrapper`
Describe the bug
Thanks for creating and maintaining the awesome spatialLIBD package. Recently, I was trying to conduct spatial registration by running registration_wrapper function on a SpatialExperiment object. I encountered the error message Error in combn(colnames(registration_model)[regis_cols], 2) : n < m (please find the reproducible example below), which I have trouble interpreting the error message and fix it.
The spatialLIBD is at v1.14.1 installed via Bioconductor version '3.18'
Provide a minimally reproducible example (reprex)
# Load packages -----------------------------------------------------------
library(here)
#> here() starts at /private/var/folders/ff/m8yvwsq51sjg43xscd3x1tmr0000gn/T/RtmpWA9JNL/reprex-774f49f557da-stony-moth
library(SpatialExperiment)
#> Loading required package: SingleCellExperiment
#> Loading required package: SummarizedExperiment
#> Loading required package: MatrixGenerics
#> Loading required package: matrixStats
#>
#> Attaching package: 'MatrixGenerics'
#> The following objects are masked from 'package:matrixStats':
#>
#> colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
#> colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
#> colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
#> colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
#> colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
#> colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
#> colWeightedMeans, colWeightedMedians, colWeightedSds,
#> colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
#> rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
#> rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
#> rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
#> rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
#> rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
#> rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
#> rowWeightedSds, rowWeightedVars
#> Loading required package: GenomicRanges
#> Loading required package: stats4
#> Loading required package: BiocGenerics
#>
#> Attaching package: 'BiocGenerics'
#> The following objects are masked from 'package:stats':
#>
#> IQR, mad, sd, var, xtabs
#> The following objects are masked from 'package:base':
#>
#> anyDuplicated, aperm, append, as.data.frame, basename, cbind,
#> colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
#> get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
#> match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
#> Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort,
#> table, tapply, union, unique, unsplit, which.max, which.min
#> Loading required package: S4Vectors
#>
#> Attaching package: 'S4Vectors'
#> The following object is masked from 'package:utils':
#>
#> findMatches
#> The following objects are masked from 'package:base':
#>
#> expand.grid, I, unname
#> Loading required package: IRanges
#> Loading required package: GenomeInfoDb
#> Loading required package: Biobase
#> Welcome to Bioconductor
#>
#> Vignettes contain introductory material; view with
#> 'browseVignettes()'. To cite Bioconductor, see
#> 'citation("Biobase")', and for packages 'citation("pkgname")'.
#>
#> Attaching package: 'Biobase'
#> The following object is masked from 'package:MatrixGenerics':
#>
#> rowMedians
#> The following objects are masked from 'package:matrixStats':
#>
#> anyMissing, rowMedians
library(spatialLIBD)
library(SingleR)
# library(tidyverse)
# Load spatialDLPFC data ---------------------------------------------------
spe <- fetch_data(type = "spatialDLPFC_Visium")
#> 2024-01-02 13:33:34.255759 loading file /Users/bguo6/Library/Caches/org.R-project.R/R/BiocFileCache/5449288a26e9_spe_filtered_final_with_clusters_and_deconvolution_results.rds%3Fdl%3D1
set.seed(1)
scr_idx <- sample(unique(spe$sample_id), 15)
tar_idx <- setdiff(unique(spe$sample_id), scr_idx)
src_spe <- spe[,spe$sample_id %in% scr_idx]
tar_spe <- spe[,spe$sample_id %in% tar_idx]
# Spatial Registration ----------------------------------------------------
## Get enrichment statistics from source ---------------------------------
sce_modeling_results <- registration_wrapper(
sce = src_spe,
# sce = src_spe,
var_registration = "BayesSpace_harmony_09",
var_sample_id = "sample_id",
gene_ensembl = "gene_id",
gene_name = "gene_name"
)
#> 2024-01-02 13:34:59.526861 make pseudobulk object
#> 2024-01-02 13:35:07.619735 dropping 0 pseudo-bulked samples that are below 'min_ncells'.
#> 2024-01-02 13:35:07.650823 drop lowly expressed genes
#> 2024-01-02 13:35:07.781492 normalize expression
#> 2024-01-02 13:35:08.545616 create model matrix
#> 2024-01-02 13:35:08.696194 run duplicateCorrelation()
#> 2024-01-02 13:35:26.808509 The estimated correlation is: 0.960849320333061
#> 2024-01-02 13:35:26.811491 computing enrichment statistics
#> 2024-01-02 13:35:28.62727 extract and reformat enrichment results
#> Error in combn(colnames(registration_model)[regis_cols], 2): n < m
Created on 2024-01-02 with reprex v2.0.2
Expected behavior
I would expect that registration_wrapper would run successfully.
R Session Information
Session info
sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#> setting value
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#> collate en_US.UTF-8
#> ctype en_US.UTF-8
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#> date 2024-01-02
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