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julia v1.9 #4

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4ad346c
julia v1.9
HaojiaWu Nov 13, 2023
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HaojiaWu Nov 15, 2023
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HaojiaWu Nov 15, 2023
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301 changes: 273 additions & 28 deletions Manifest.toml
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6 changes: 6 additions & 0 deletions Project.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -16,20 +16,24 @@ DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
DataFramesMeta = "1313f7d8-7da2-5740-9ea0-a2ca25f37964"
Distances = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7"
Distributed = "8ba89e20-285c-5b6f-9357-94700520ee1b"
FFTW = "7a1cc6ca-52ef-59f5-83cd-3a7055c09341"
FileIO = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549"
Folds = "41a02a25-b8f0-4f67-bc48-60067656b558"
GZip = "92fee26a-97fe-5a0c-ad85-20a5f3185b63"
GeneticsMakie = "8ca62643-82d8-47b5-a233-a06d1654fb35"
Glob = "c27321d9-0574-5035-807b-f59d2c89b15c"
Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6"
Grep = "775960c6-9b90-5df0-b405-1e337feb71e5"
HDF5 = "f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f"
HTTP = "cd3eb016-35fb-5094-929b-558a96fad6f3"
HypothesisTests = "09f84164-cd44-5f33-b23f-e6b0d136a0d5"
IJulia = "7073ff75-c697-5162-941a-fcdaad2a7d2a"
ImageCore = "a09fc81d-aa75-5fe9-8630-4744c3626534"
ImageMorphology = "787d08f9-d448-5407-9aad-5290dd7ab264"
Images = "916415d5-f1e6-5110-898d-aaa5f9f070e0"
JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
KernelDensity = "5ab0869b-81aa-558d-bb23-cbf5423bbe9b"
Leiden = "e5cf005d-d64d-44d4-821e-2384bf4ace83"
LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
Loess = "4345ca2d-374a-55d4-8d30-97f9976e7612"
Expand All @@ -38,6 +42,7 @@ MatrixMarket = "4d4711f2-db25-561a-b6b3-d35e7d4047d3"
MultipleTesting = "f8716d33-7c4a-5097-896f-ce0ecbd3ef6b"
MultivariateStats = "6f286f6a-111f-5878-ab1e-185364afe411"
NearestNeighborDescent = "dd2c4c9e-a32f-5b2f-b342-08c2f244fce8"
NearestNeighbors = "b8a86587-4115-5ab1-83bc-aa920d37bbce"
Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
PlotlyJS = "f0f68f2c-4968-5e81-91da-67840de0976a"
Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
Expand All @@ -48,6 +53,7 @@ PyCallUtils = "02651160-e6c3-11e9-0e2a-551f75d9519e"
RCall = "6f49c342-dc21-5d91-9882-a32aef131414"
Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
RollingFunctions = "b0e4dd01-7b14-53d8-9b45-175a3e362653"
SimpleWeightedGraphs = "47aef6b3-ad0c-573a-a1e2-d07658019622"
SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
Expand Down
10 changes: 10 additions & 0 deletions src/CellScopes.jl
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Expand Up @@ -54,6 +54,14 @@ using GeneticsMakie
using Arrow
using HDF5
using PyCallUtils
import FFTW
import ImageMorphology
import Graphs
using NearestNeighbors: KDTree, knn
using SimpleWeightedGraphs
using StatsBase: countmap
using KernelDensity
using Graphs: src, dst

include("scrna/objects.jl")
include("spatial/sp_objects.jl")
Expand All @@ -70,4 +78,6 @@ include("spatial/sp_processing.jl")
include("scatac/atac_processing.jl")
include("scatac/atac_plots.jl")
include("scatac/atac_utils.jl")
include("spatial/baysor_boundary.jl")

end
7 changes: 5 additions & 2 deletions src/properties.jl
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Expand Up @@ -56,7 +56,7 @@ function Base.show(io::IO, count::AbstractCount)
[println("- ", string(i)) for i in fieldnames(typeof(count))]
end

function Base.show(io::IO, obj_type::Union{AbstractDimReduction, ClusteringObject, VariableGeneObject, UndefinedObject, SpaImputeObj, VisiumImgObject, SpaCountObj,SpaMetaObj})
function Base.show(io::IO, obj_type::Union{AbstractDimReduction, ClusteringObject, VariableGeneObject, UndefinedObject, SpaImputeObj, VisiumImgObject, SpaCountObj,SpaMetaObj,SpaImageObj})
println(io, string(typeof(obj_type)))
println("All fields:")
[println("- ", string(i)) for i in fieldnames(typeof(obj_type))]
Expand All @@ -76,10 +76,11 @@ matchtype(field) = @match field begin
spMeta::SpaMetaObj => println("- Spatial metadata")
spCoord::SpaCoordObj => println("- Spatial coordiantes")
fragment::FragmentObject => println("- Fragment data")
imgObject::SpaImageObj => println("- Image data")
uns::UndefinedObject => println("- Undefined slot")
end

function Base.show(io::IO, sp_obj::Union{ImagingSpatialObject, CartanaObject, VisiumObject, XeniumObject, MerfishObject, SlideseqObject, STARmapObject, seqFishObject})
function Base.show(io::IO, sp_obj::Union{ImagingSpatialObject, CartanaObject, VisiumObject, XeniumObject, MerfishObject, SlideseqObject, STARmapObject, seqFishObject, StereoSeqObject})
if isa(sp_obj, ImagingSpatialObject)
println(io, "ImagingSpatialObject in CellScopes.jl")
elseif isa(sp_obj, CartanaObject)
Expand All @@ -94,6 +95,8 @@ function Base.show(io::IO, sp_obj::Union{ImagingSpatialObject, CartanaObject, Vi
println(io, "seqFishObject in CellScopes.jl")
elseif isa(sp_obj, SlideseqObject)
println(io, "SlideseqObject in CellScopes.jl")
elseif isa(sp_obj, StereoSeqObject)
println(io, "StereoSeqObject in CellScopes.jl")
else
println(io, "VisiumObject in CellScopes.jl")
end
Expand Down
22 changes: 11 additions & 11 deletions src/scrna/processing.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@ function normalize_object(ct_obj::RawCountObject; scale_factor = 10000, norm_met
return norm_obj
end

function normalize_object(sc_obj::Union{scRNAObject, VisiumObject,ImagingSpatialObject, CartanaObject, XeniumObject, MerfishObject, SlideseqObject, STARmapObject, seqFishObject}; scale_factor = 10000, norm_method = "logarithm", pseudocount = 1)
function normalize_object(sc_obj::Union{scRNAObject, VisiumObject,ImagingSpatialObject, CartanaObject, XeniumObject, MerfishObject, SlideseqObject, STARmapObject, seqFishObject, StereoSeqObject}; scale_factor = 10000, norm_method = "logarithm", pseudocount = 1)
norm_obj = normalize_object(sc_obj.rawCount; scale_factor = scale_factor, norm_method = norm_method, pseudocount = pseudocount)
sc_obj.normCount = norm_obj
if isa(sc_obj, Union{MerfishObject, CartanaObject, XeniumObject})
Expand Down Expand Up @@ -42,7 +42,7 @@ function scale_object(ct_obj::NormCountObject; features::Union{Vector{String}, N
return scale_obj
end

function scale_object(sc_obj::Union{scRNAObject, VisiumObject, ImagingSpatialObject, CartanaObject, XeniumObject,MerfishObject, SlideseqObject, STARmapObject, seqFishObject}; features::Union{Vector{String}, Nothing}=nothing, scale_max = 10.0, do_scale::Bool = true, do_center::Bool = true)
function scale_object(sc_obj::Union{scRNAObject, VisiumObject, ImagingSpatialObject, CartanaObject, XeniumObject,MerfishObject, SlideseqObject, STARmapObject, seqFishObject, StereoSeqObject}; features::Union{Vector{String}, Nothing}=nothing, scale_max = 10.0, do_scale::Bool = true, do_center::Bool = true)
scale_obj = scale_object(sc_obj.normCount; features = features, scale_max=scale_max, do_scale=do_scale, do_center=do_center)
sc_obj.scaleCount = scale_obj
return sc_obj
Expand Down Expand Up @@ -72,14 +72,14 @@ function find_variable_genes(ct_mtx::RawCountObject; nFeatures::Int64 = 2000, sp
return vst_data, Features
end

function find_variable_genes(sc_obj::Union{scRNAObject, VisiumObject, ImagingSpatialObject, CartanaObject, XeniumObject,MerfishObject, SlideseqObject, STARmapObject, seqFishObject}; nFeatures::Int64 = 2000, span::Float64 = 0.3)
function find_variable_genes(sc_obj::Union{scRNAObject, VisiumObject, ImagingSpatialObject, CartanaObject, XeniumObject,MerfishObject, SlideseqObject, STARmapObject, seqFishObject, StereoSeqObject}; nFeatures::Int64 = 2000, span::Float64 = 0.3)
vst_data, Features = find_variable_genes(sc_obj.rawCount; nFeatures = nFeatures, span = span)
var_obj = VariableGeneObject(Features, vst_data)
sc_obj.varGene = var_obj
return sc_obj
end

function run_pca(sc_obj::Union{scRNAObject, VisiumObject, ImagingSpatialObject, CartanaObject, XeniumObject,MerfishObject, SlideseqObject, STARmapObject, seqFishObject}; method=:svd, pratio = 1, maxoutdim = 10)
function run_pca(sc_obj::Union{scRNAObject, VisiumObject, ImagingSpatialObject, CartanaObject, XeniumObject,MerfishObject, SlideseqObject, STARmapObject, seqFishObject, StereoSeqObject}; method=:svd, pratio = 1, maxoutdim = 10)
features = sc_obj.varGene.var_gene
if length(sc_obj.scaleCount.gene_name) == length(sc_obj.rawCount.gene_name)
new_count = subset_count(sc_obj.scaleCount; genes = features)
Expand All @@ -99,7 +99,7 @@ function run_pca(sc_obj::Union{scRNAObject, VisiumObject, ImagingSpatialObject,
return sc_obj
end

function run_clustering_atlas(sc_obj::Union{scRNAObject, VisiumObject, ImagingSpatialObject, CartanaObject, XeniumObject, scATACObject,MerfishObject, SlideseqObject, STARmapObject, seqFishObject}; n_neighbors=30, metric=CosineDist(), res= 0.06, seed_use=1234)
function run_clustering_atlas(sc_obj::Union{scRNAObject, VisiumObject, ImagingSpatialObject, CartanaObject, XeniumObject, scATACObject,MerfishObject, SlideseqObject, STARmapObject, seqFishObject, StereoSeqObject}; n_neighbors=30, metric=CosineDist(), res= 0.06, seed_use=1234)
if isdefined(sc_obj.dimReduction, :umap)
indices = sc_obj.dimReduction.umap.knn_data
else
Expand Down Expand Up @@ -147,7 +147,7 @@ function run_clustering_atlas(sc_obj::Union{scRNAObject, VisiumObject, ImagingSp
return sc_obj
end

function run_clustering_small(sc_obj::Union{scRNAObject, VisiumObject, ImagingSpatialObject, CartanaObject, XeniumObject, scATACObject, MerfishObject, SlideseqObject, STARmapObject, seqFishObject}; n_neighbors=30, metric=CosineDist(), res= 0.06, seed_use=1234)
function run_clustering_small(sc_obj::Union{scRNAObject, VisiumObject, ImagingSpatialObject, CartanaObject, XeniumObject, scATACObject, MerfishObject, SlideseqObject, STARmapObject, seqFishObject, StereoSeqObject}; n_neighbors=30, metric=CosineDist(), res= 0.06, seed_use=1234)
knn_data = [collect(i) for i in eachrow(sc_obj.dimReduction.pca.cell_embedding)]
graph = nndescent(knn_data, n_neighbors, metric)
indices, dist_mat = knn_matrices(graph);
Expand Down Expand Up @@ -192,7 +192,7 @@ function run_clustering_small(sc_obj::Union{scRNAObject, VisiumObject, ImagingSp
return sc_obj
end

function run_clustering(sc_obj::Union{scRNAObject, VisiumObject, ImagingSpatialObject, CartanaObject, XeniumObject, scATACObject, MerfishObject, SlideseqObject, STARmapObject, seqFishObject}; n_neighbors=30, metric=CosineDist(), res= 0.06, seed_use=1234)
function run_clustering(sc_obj::Union{scRNAObject, VisiumObject, ImagingSpatialObject, CartanaObject, XeniumObject, scATACObject, MerfishObject, SlideseqObject, STARmapObject, seqFishObject, StereoSeqObject}; n_neighbors=30, metric=CosineDist(), res= 0.06, seed_use=1234)
n = size(sc_obj.rawCount.count_mtx, 2)
if n < 10000
obj = run_clustering_small(sc_obj; n_neighbors=n_neighbors, metric=metric, res= res, seed_use=seed_use)
Expand All @@ -203,7 +203,7 @@ function run_clustering(sc_obj::Union{scRNAObject, VisiumObject, ImagingSpatialO
end
end

function run_tsne(sc_obj::Union{scRNAObject, VisiumObject, ImagingSpatialObject, CartanaObject, XeniumObject, scATACObject, MerfishObject, SlideseqObject, STARmapObject, seqFishObject}; ndim::Int64 = 2, dims_use = 1:10, max_iter::Int64 = 2000, perplexit::Real = 30.0, pca_init::Bool = true, seed_use::Int64 = 1234)
function run_tsne(sc_obj::Union{scRNAObject, VisiumObject, ImagingSpatialObject, CartanaObject, XeniumObject, scATACObject, MerfishObject, SlideseqObject, STARmapObject, seqFishObject, StereoSeqObject}; ndim::Int64 = 2, dims_use = 1:10, max_iter::Int64 = 2000, perplexit::Real = 30.0, pca_init::Bool = true, seed_use::Int64 = 1234)
Random.seed!(seed_use)
pca_mat = sc_obj.dimReduction.pca.cell_embedding
pca_mat = pca_mat[:, dims_use]
Expand All @@ -215,7 +215,7 @@ function run_tsne(sc_obj::Union{scRNAObject, VisiumObject, ImagingSpatialObject,
return sc_obj
end

function run_umap(sc_obj::Union{scRNAObject, VisiumObject, ImagingSpatialObject, CartanaObject, XeniumObject, scATACObject,MerfishObject, SlideseqObject, STARmapObject, seqFishObject}; ndim::Int64 = 2, dims_use = 1:10, n_neighbors::Int64 = 30, n_epochs=300, init = :spectral, metric = CosineDist(), min_dist::Real = 0.4, seed_use::Int64 = 1234)
function run_umap(sc_obj::Union{scRNAObject, VisiumObject, ImagingSpatialObject, CartanaObject, XeniumObject, scATACObject,MerfishObject, SlideseqObject, STARmapObject, seqFishObject, StereoSeqObject}; ndim::Int64 = 2, dims_use = 1:10, n_neighbors::Int64 = 30, n_epochs=300, init = :spectral, metric = CosineDist(), min_dist::Real = 0.4, seed_use::Int64 = 1234)
Random.seed!(seed_use)
pca_mat = sc_obj.dimReduction.pca.cell_embedding
pca_mat = pca_mat[:, dims_use]
Expand All @@ -233,7 +233,7 @@ function run_umap(sc_obj::Union{scRNAObject, VisiumObject, ImagingSpatialObject,
return sc_obj
end

function find_markers(sc_obj::Union{scRNAObject, VisiumObject, ImagingSpatialObject, CartanaObject, XeniumObject, scATACObject, MerfishObject, SlideseqObject, STARmapObject, seqFishObject}; cluster_1::Union{String, Nothing}=nothing, cluster_2::Union{String, Nothing}=nothing,
function find_markers(sc_obj::Union{scRNAObject, VisiumObject, ImagingSpatialObject, CartanaObject, XeniumObject, scATACObject, MerfishObject, SlideseqObject, STARmapObject, seqFishObject, StereoSeqObject}; cluster_1::Union{String, Nothing}=nothing, cluster_2::Union{String, Nothing}=nothing,
anno::Union{String, Symbol}="cluster", expr_cutoff=0.0, min_pct=0.1, p_cutoff = 0.05, only_pos = true)
if isa(cluster_1, Nothing)
error("Please provide the name of the cell cluster for which you wish to obtain the differential genes. The \"cluster_1\" parameter cannot be left blank.")
Expand Down Expand Up @@ -275,7 +275,7 @@ function find_markers(sc_obj::Union{scRNAObject, VisiumObject, ImagingSpatialObj
return test_result
end

function find_all_markers(sc_obj::Union{scRNAObject, VisiumObject, ImagingSpatialObject, CartanaObject, XeniumObject, scATACObject,MerfishObject, SlideseqObject, STARmapObject, seqFishObject}; anno::Union{String, Symbol}="cluster", expr_cutoff=0.0, min_pct=0.1, p_cutoff = 0.05, only_pos = true)
function find_all_markers(sc_obj::Union{scRNAObject, VisiumObject, ImagingSpatialObject, CartanaObject, XeniumObject, scATACObject,MerfishObject, SlideseqObject, STARmapObject, seqFishObject, StereoSeqObject}; anno::Union{String, Symbol}="cluster", expr_cutoff=0.0, min_pct=0.1, p_cutoff = 0.05, only_pos = true)
if isa(anno, String)
anno = Symbol(anno)
end
Expand Down
20 changes: 10 additions & 10 deletions src/scrna/utils.jl
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Original file line number Diff line number Diff line change
@@ -1,8 +1,8 @@
colSum(mtx::AbstractMatrix{<:Real}) = sum(mtx, dims=1)
rowSum(mtx::AbstractMatrix{<:Real}) = sum(mtx, dims=2)
rownames(sc_obj::Union{scRNAObject, VisiumObject, ImagingSpatialObject, CartanaObject, XeniumObject, MerfishObject, SlideseqObject, seqFishObject, STARmapObject}) = sc_obj.rawCount.gene_name
rownames(sc_obj::Union{scRNAObject, VisiumObject, ImagingSpatialObject, CartanaObject, XeniumObject, MerfishObject, SlideseqObject, seqFishObject, STARmapObject, StereoSeqObject}) = sc_obj.rawCount.gene_name
rownames(sc_obj::scATACObject) = sc_obj.rawCount.peak_name
colnames(sc_obj::Union{scRNAObject, VisiumObject, ImagingSpatialObject, CartanaObject, XeniumObject, scATACObject, MerfishObject, SlideseqObject, seqFishObject, STARmapObject}) = sc_obj.rawCount.cell_name
colnames(sc_obj::Union{scRNAObject, VisiumObject, ImagingSpatialObject, CartanaObject, XeniumObject, scATACObject, MerfishObject, SlideseqObject, seqFishObject, STARmapObject, StereoSeqObject}) = sc_obj.rawCount.cell_name
rownames(ct_mat::AbstractCount) = ct_mat.gene_name
colnames(ct_mat::AbstractCount) = ct_mat.cell_name

Expand Down Expand Up @@ -86,7 +86,7 @@ function subset_count(ct_obj::T;
return new_obj
end

function extract_cluster_count(sc_obj::Union{scRNAObject, VisiumObject, ImagingSpatialObject, CartanaObject, XeniumObject, MerfishObject, SlideseqObject, seqFishObject, STARmapObject}, cl; count_type = "norm", anno = Union{String, Symbol}="cluster")
function extract_cluster_count(sc_obj::Union{scRNAObject, VisiumObject, ImagingSpatialObject, CartanaObject, XeniumObject, MerfishObject, SlideseqObject, seqFishObject, STARmapObject, StereoSeqObject}, cl; count_type = "norm", anno = Union{String, Symbol}="cluster")
df = sc_obj.clustData.clustering
if isa(anno, String)
anno = Symbol(anno)
Expand Down Expand Up @@ -150,12 +150,12 @@ function jitter(x)
end
end

function variable_genes(sc_obj::Union{scRNAObject, VisiumObject, ImagingSpatialObject, CartanaObject, XeniumObject, MerfishObject, SlideseqObject, seqFishObject, STARmapObject})
function variable_genes(sc_obj::Union{scRNAObject, VisiumObject, ImagingSpatialObject, CartanaObject, XeniumObject, MerfishObject, SlideseqObject, seqFishObject, STARmapObject, StereoSeqObject})
vargenes = pbmc.varGene.var_gene
return vargenes
end

function update_object(sp_obj::Union{scRNAObject, VisiumObject, ImagingSpatialObject, CartanaObject, XeniumObject, MerfishObject, SlideseqObject, seqFishObject, STARmapObject})
function update_object(sp_obj::Union{scRNAObject, VisiumObject, ImagingSpatialObject, CartanaObject, XeniumObject, MerfishObject, SlideseqObject, seqFishObject, STARmapObject, StereoSeqObject})
cells = colnames(sp_obj)
genes = rownames(sp_obj)
all_cells = sp_obj.metaData.Cell_id
Expand Down Expand Up @@ -189,7 +189,7 @@ function update_object(sp_obj::Union{scRNAObject, VisiumObject, ImagingSpatialOb
sp_obj.clustData.adj_mat = sp_obj.clustData.adj_mat[check_cell, check_cell]
end
end
if isa(sp_obj, Union{ImagingSpatialObject, CartanaObject, XeniumObject, MerfishObject, seqFishObject, STARmapObject})
if isa(sp_obj, Union{ImagingSpatialObject, CartanaObject, XeniumObject, MerfishObject, seqFishObject, STARmapObject, StereoSeqObject})
println("Updating spatial data...")
sp_obj.spmetaData.cell = filter(:cell => ∈(cell_set), sp_obj.spmetaData.cell)
sp_obj.spmetaData.molecule = filter(:cell => ∈(cell_set), sp_obj.spmetaData.molecule)
Expand Down Expand Up @@ -250,13 +250,13 @@ function update_object(sp_obj::Union{scRNAObject, VisiumObject, ImagingSpatialOb
return sp_obj
end

function subset_object(sp_obj::Union{scRNAObject, VisiumObject, ImagingSpatialObject, CartanaObject, XeniumObject, MerfishObject, SlideseqObject, seqFishObject, STARmapObject}; cells = nothing, genes = nothing)
function subset_object(sp_obj::Union{scRNAObject, VisiumObject, ImagingSpatialObject, CartanaObject, XeniumObject, MerfishObject, SlideseqObject, seqFishObject, STARmapObject, StereoSeqObject}; cells = nothing, genes = nothing)
sp_obj.rawCount = subset_count(sp_obj.rawCount; genes = genes, cells = cells)
sp_obj = update_object(sp_obj)
return sp_obj
end

function check_dim(sp_obj::Union{scRNAObject, VisiumObject,ImagingSpatialObject, CartanaObject, XeniumObject, MerfishObject, seqFishObject, STARmapObject}, field_name::Union{Symbol, String})
function check_dim(sp_obj::Union{scRNAObject, VisiumObject,ImagingSpatialObject, CartanaObject, XeniumObject, MerfishObject, seqFishObject, STARmapObject, StereoSeqObject}, field_name::Union{Symbol, String})
if isa(field_name, String)
field_name = Symbol(field_name)
end
Expand All @@ -265,7 +265,7 @@ function check_dim(sp_obj::Union{scRNAObject, VisiumObject,ImagingSpatialObject,
return check_length
end

function update_count(sp_obj::Union{scRNAObject, VisiumObject, ImagingSpatialObject, CartanaObject, XeniumObject, MerfishObject, seqFishObject, STARmapObject}, ct_name::Union{Symbol, String})
function update_count(sp_obj::Union{scRNAObject, VisiumObject, ImagingSpatialObject, CartanaObject, XeniumObject, MerfishObject, seqFishObject, STARmapObject, StereoSeqObject}, ct_name::Union{Symbol, String})
cell_id = colnames(sp_obj)
gene_id = rownames(sp_obj)
if isa(ct_name, String)
Expand Down Expand Up @@ -337,7 +337,7 @@ function sparse_r_to_jl(counts::RObject{S4Sxp})
return julia_sparse_matrix
end

function annotate_cells(sp::Union{scRNAObject, VisiumObject, ImagingSpatialObject, CartanaObject, XeniumObject, MerfishObject, SlideseqObject, seqFishObject, STARmapObject}, cell_map::Dict; old_id_name::Union{String, Symbol}="cluster", new_id_name::Union{String, Symbol}="celltype")
function annotate_cells(sp::Union{scRNAObject, VisiumObject, ImagingSpatialObject, CartanaObject, XeniumObject, MerfishObject, SlideseqObject, seqFishObject, STARmapObject, StereoSeqObject}, cell_map::Dict; old_id_name::Union{String, Symbol}="cluster", new_id_name::Union{String, Symbol}="celltype")
sp.metaData = map_values(sp.metaData, old_id_name , new_id_name, collect(keys(cell_map)), collect(values(cell_map)))
if isa(sp, Union{CartanaObject, MerfishObject, XeniumObject, seqFishObject, STARmapObject})
sp.spmetaData.cell[!, old_id_name] = sp.metaData.cell[!, old_id_name]
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