Issues with running the STARmap example

[HongBei-SS]

Hi, when I run the STARmap example, the following problem occurs

baysor preview -x 'x' -y 'y' -g 'gene' -c configs/starmap.toml -o output_dapi molecules.csv
[19:16:50] Info: (2023-09-13) Run Baysor v0.6.2
[19:16:50] Info: Loading data...
[19:16:52] Info: Loaded 949459 transcripts
[19:16:53] Info: Estimating noise level
[19:17:15] Info: Done
[19:17:15] Info: Estimating local colors
[19:17:47] Warning: n=10000, which is > length(high_conf_ids) (0)
└ Baysor.Processing /home/viktor_petukhov/.julia/dev/Baysor/src/processing/data_processing/initialization.jl:180
ERROR: ArgumentError: size(X, 2) must be greater than n_neighbors and n_neighbors must be greater than 0
Stacktrace:
[1] UMAP.UMAP_(X::Matrix{Float32}, n_components::Int64; n_neighbors::Int64, metric::Distances.Euclidean, n_epochs::Int64, learning_rate::Int64, init::Symbol, min_dist::Float64, spread::Float64, set_operation_ratio::Int64, local_connectivity::Int64, repulsion_strength::Int64, neg_sample_rate::Int64, a::Nothing, b::Nothing)
@ UMAP /home/viktor_petukhov/.julia/packages/UMAP/oqkOM/src/umap_.jl:94
[2] UMAP_
@ /home/viktor_petukhov/.julia/packages/UMAP/oqkOM/src/umap_.jl:77 [inlined]
[3] #umap#7
@ /home/viktor_petukhov/.julia/packages/UMAP/oqkOM/src/umap_.jl:45 [inlined]
[4] umap
@ /home/viktor_petukhov/.julia/packages/UMAP/oqkOM/src/umap_.jl:43 [inlined]
[5] fit(::Type{Baysor.Processing.UmapFit}, x::Matrix{Float32}; n_components::Int64, nn_interpolate::Int64, spread::Float64, min_dist::Float64, metric::Distances.Euclidean, kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
@ Baysor.Processing /home/viktor_petukhov/.julia/dev/Baysor/src/processing/data_processing/umap_wrappers.jl:22
[6] fit
@ /home/viktor_petukhov/.julia/dev/Baysor/src/processing/data_processing/umap_wrappers.jl:17 [inlined]
[7] gene_composition_color_embedding(pca::Matrix{Float32}, confidence::Vector{Float64}; normalize::Bool, sample_size::Int64, seed::Int64, kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
@ Baysor.Processing /home/viktor_petukhov/.julia/dev/Baysor/src/processing/data_processing/neighborhood_composition.jl:128
[8] gene_composition_color_embedding(pca::Matrix{Float32}, confidence::Vector{Float64})
@ Baysor.Processing /home/viktor_petukhov/.julia/dev/Baysor/src/processing/data_processing/neighborhood_composition.jl:116
[9] gene_composition_colors(df_spatial::DataFrames.DataFrame, k::Int64; method::Symbol, n_pcs::Int64, kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
@ Baysor.Processing /home/viktor_petukhov/.julia/dev/Baysor/src/processing/data_processing/neighborhood_composition.jl:165
[10] gene_composition_colors(df_spatial::DataFrames.DataFrame, k::Int64)
@ Baysor.Processing /home/viktor_petukhov/.julia/dev/Baysor/src/processing/data_processing/neighborhood_composition.jl:160
[11] preview(coordinates::String; config::Baysor.Utils.RunOptions, x_column::String, y_column::String, z_column::String, gene_column::String, min_molecules_per_cell::Int64, output::String)
@ Baysor.CommandLine /home/viktor_petukhov/.julia/dev/Baysor/src/cli/preview.jl:63
[12] command_main(ARGS::Vector{String})
@ Baysor.CommandLine /home/viktor_petukhov/.julia/packages/Comonicon/HDhA6/src/codegen/julia.jl:343
[13] command_main
@ /home/viktor_petukhov/.julia/packages/Comonicon/HDhA6/src/codegen/julia.jl:90 [inlined]
[14] julia_main()
@ Baysor.CommandLine /home/viktor_petukhov/.julia/packages/Comonicon/HDhA6/src/frontend/cast.jl:481
[15] julia_main(; kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
@ Baysor /home/viktor_petukhov/.julia/dev/Baysor/src/Baysor.jl:42
[16] julia_main()
@ Baysor /home/viktor_petukhov/.julia/dev/Baysor/src/Baysor.jl:42
[17] top-level scope
@ none:1

[VPetukhov]

Looks like a duplicate of #90.