clonalCluster error

[Liripo]

Run the following code according to the tutorial and report an error

#Adding patient information
scRep_example$Patient <- substr(scRep_example$orig.ident, 1,3)

#Adding type information
scRep_example$Type <- substr(scRep_example$orig.ident, 4,4)

#Define color palette 
colorblind_vector <- hcl.colors(n=7, palette = "inferno", fixup = TRUE)

scRep_example <- clonalCluster(scRep_example, 
                               chain = "TRA", 
                               sequence = "aa", 
                               threshold = 0.85, 
                               group.by = "Patient")

The error is:

Error in eval(e, x, parent.frame()) : object 'cloneSize' not found

sessioninfo

R version 4.4.1 (2024-06-14)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 22.04.4 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               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    LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

time zone: Etc/UTC
tzcode source: system (glibc)

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] patchwork_1.2.0    scRepertoire_2.0.4 ggplot2_3.5.1     

[ncborcherding]

@Liripo

You will need to attach the clonal information to the single-cell object before clustering. You can do that by using:

data("contig_list") 
combined.TCR <- combineTCR(contig_list, 
                           samples = c("P17B", "P17L", "P18B", "P18L", 
                                       "P19B","P19L", "P20B", "P20L"))

scRep_example <- combineExpression(combined.TCR, 
                                   scRep_example, 
                                   cloneCall="gene", 
                                   group.by = "sample")