doLeidenCluster error

[zglu]

Hi,

I used the Giotto docker image and encountered an error when doing doLeidenCluster():

Fatal error at src/core/vector.c:483 : Assertion failed: v->stor_begin != NULL

What could be the reason please?

Here are the commands that I ran:

library(Giotto)
library(Seurat)

expression_matrix = readExprMatrix("seqfish_field_expr.txt")
cell_locations = data.table::fread("seqfish_field_locs.txt")

my_giotto_object = createGiottoObject(raw_exprs = expression_matrix, spatial_locs = cell_locations)

my_giotto_object <- filterGiotto(gobject = my_giotto_object, 
                                 expression_threshold = 1, 
                                 gene_det_in_min_cells = 10, 
                                 min_det_genes_per_cell = 5)

my_giotto_object <- normalizeGiotto(gobject = my_giotto_object, scalefactor = 6000, verbose = T)

my_giotto_object <- addStatistics(gobject = my_giotto_object)
my_giotto_object <- adjustGiottoMatrix(gobject = my_giotto_object, 
                                   expression_values = c('normalized'),
                                   covariate_columns = c('nr_genes', 'total_expr'))

head(my_giotto_object@cell_metadata)

my_giotto_object <- calculateHVG(gobject = my_giotto_object, save_plot=TRUE)
my_giotto_object <- runPCA(gobject = my_giotto_object)
my_giotto_object <- runUMAP(my_giotto_object, dimensions_to_use = 1:10)

my_giotto_object <- createNearestNetwork(gobject = my_giotto_object, dimensions_to_use = 1:10, k = 5)
my_giotto_object = doLeidenCluster(my_giotto_object, name = 'leiden_clus')

Giotto version is 1.1.2 in the docker image. But doLouvainCluster() works.

Thanks, Zhigang

[GCatatGC]

I also got another issue when doing doLeidenCluster(): Error in py_run_file_impl(file, local, convert) : ImportError: DLL load failed while importing _c_leiden: The specified procedure could not be found.

[josschavezf]

Hi @zglu and @GCatatGC, thanks a lot for your feedback. I'll look at the docker image and see if updating it solves the issue. I'll be back to you by tomorrow morning. Thanks for your patience

[zglu]

Hi @josschavezf, that's a good hint. I just tried to upgrade the igraph python-igraph leidenalg libraries and it does solves the problem. Thanks a lot!

[RubD]

Thanks @josschavezf for help fixing this issue. I've moved the issue from @GCatatGC to a new issue and will close this one.