Merge pull request #3 from niklasmueboe/dev

Test + new name
niklasmueboe · Jun 18, 2024 · 80bf49b · 80bf49b
2 parents e3a0e71 + fdfaac5
commit 80bf49b
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diff --git a/Project.toml b/Project.toml
@@ -1,4 +1,4 @@
-name    = "StereoSSAM"
+name    = "Sainsc"
 uuid    = "4c4340ea-7f9e-46b4-8512-61f1f6c41a11"
 authors = ["Niklas Müller-Bötticher <[email protected]>"]
 version = "0.1.0"
@@ -28,15 +28,18 @@ CellScopesExt                 = "CellScopes"
 SingleCellProjectionsExt      = "SingleCellProjections"
 
 [compat]
-BlockArrays       = "0.16,1"
-CSV               = "0.10"
-CategoricalArrays = "0.9,0.10"
-DataFrames        = "1"
-ImageFiltering    = "0.7"
-LinearAlgebra     = "1"
-Muon              = "0.2"
-OffsetArrays      = "1.11"
-PooledArrays      = "1"
-SparseArrays      = "1"
-Unzip             = "0.2"
-julia             = "1.9"
+AutomaticSingleCellToolbox = "0.9"
+BlockArrays                = "0.16,1"
+CSV                        = "0.10"
+CategoricalArrays          = "0.9,0.10"
+CellScopes                 = "1"
+DataFrames                 = "1"
+ImageFiltering             = "0.7"
+LinearAlgebra              = "1"
+Muon                       = "0.2"
+OffsetArrays               = "1.11"
+PooledArrays               = "1"
+SparseArrays               = "1"
+SingleCellProjections      = "0.3"
+Unzip                      = "0.2"
+julia                      = "1.9"
diff --git a/README.md b/README.md
@@ -1,28 +1,34 @@
-# StereoSSAM.jl
+# Sainsc.jl
 
-[![Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://niklasmueboe.github.io/StereoSSAM.jl/stable)
-[![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://niklasmueboe.github.io/StereoSSAM.jl/dev)
+[![Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://niklasmueboe.github.io/Sainsc.jl/stable)
+[![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://niklasmueboe.github.io/Sainsc.jl/dev)
 [![Code Style: Blue](https://img.shields.io/badge/code%20style-blue-4495d1.svg)](https://github.com/invenia/BlueStyle)
 [![Aqua QA](https://raw.githubusercontent.com/JuliaTesting/Aqua.jl/master/badge.svg)](https://github.com/JuliaTesting/Aqua.jl)
 
+/ˈsaiəns/
+
+_"**S**egmentation-free **A**nalysis of **In S**itu **C**apture data"_
+or alternatively
+"_**S**tupid **A**cronyms **In Sc**ience_"
+
 ## Installation
 
 The package can be installed with the Julia package manager.
 From the Julia REPL, type `]` to enter the `Pkg` REPL mode and run:
 
 ```
-pkg> add StereoSSAM
+pkg> add Sainsc
 ```
 
 Or, alternatively, via the `Pkg` API:
 
 ```julia
 using Pkg
-Pkg.add("StereoSSAM")
+Pkg.add("Sainsc")
 ```
 
 ## Documentation
 
-The documentation for StereoSSAM.jl is available [here](https://niklasmueboe.github.io/StereoSSAM.jl/stable).
-It includes the [Reference API](https://niklasmueboe.github.io/StereoSSAM.jl/stable/api)
-as well as an [example analysis](https://niklasmueboe.github.io/StereoSSAM.jl/stable/examples/ExampleAnalysis).
+The documentation for Sainsc.jl is available [here](https://niklasmueboe.github.io/Sainsc.jl/stable).
+It includes the [Reference API](https://niklasmueboe.github.io/Sainsc.jl/stable/api)
+as well as an [example analysis](https://niklasmueboe.github.io/Sainsc.jl/stable/examples/ExampleAnalysis).
diff --git a/docs/Project.toml b/docs/Project.toml
@@ -1,7 +1,7 @@
 [deps]
 Documenter           = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 DocumenterInterLinks = "d12716ef-a0f6-4df4-a9f1-a5a34e75c656"
-StereoSSAM           = "4c4340ea-7f9e-46b4-8512-61f1f6c41a11"
+Sainsc               = "4c4340ea-7f9e-46b4-8512-61f1f6c41a11"
 
 [compat]
 Documenter           = "1.3"

diff --git a/docs/make.jl b/docs/make.jl
@@ -1,20 +1,17 @@
 using Documenter
 using DocumenterInterLinks
-using StereoSSAM
+using Sainsc
 
 links = InterLinks(
     # "CategoricalArrays" => "https://categoricalarrays.juliadata.org/stable/",
     # "DataFrames" => "https://dataframes.juliadata.org/stable/",
     # "OffsetArrays" => "https://juliaarrays.github.io/OffsetArrays.jl/stable/",
     "Muon" => "https://scverse.org/Muon.jl/dev/",
-    "SparseArrays" => (
-        "https://docs.julialang.org/en/v1/stdlib/SparseArrays/",
-        "https://docs.julialang.org/en/v1/objects.inv",
-    ),
+    "SparseArrays" => "https://docs.julialang.org/en/v1/",
 )
 
 makedocs(;
-    sitename="StereoSSAM.jl",
+    sitename="Sainsc.jl",
     pages=[
         "Home" => "index.md",
         "Example analysis" => "examples/ExampleAnalysis.md",
@@ -25,4 +22,4 @@ makedocs(;
     format=Documenter.HTML(; size_threshold_ignore=["examples/ExampleAnalysis.md"]),
 )
 
-deploydocs(; repo="github.com/niklasmueboe/StereoSSAM.jl.git")
+deploydocs(; repo="github.com/niklasmueboe/Sainsc.jl.git")
diff --git a/docs/src/api.md b/docs/src/api.md
@@ -1,6 +1,6 @@
 # Reference API
 
-Documentation for `StereoSSAM.jl`'s public interface.
+Documentation for `Sainsc.jl`'s public interface.
 
 ## Index
 
@@ -12,10 +12,10 @@ Pages = ["api.md"]
 
 ```@autodocs
 Modules = [
-    StereoSSAM.GridCount,
-    StereoSSAM.IO,
-    StereoSSAM.Utils,
-    StereoSSAM.KDE,
-    StereoSSAM.LocalMax,
+    Sainsc.GridCount,
+    Sainsc.IO,
+    Sainsc.Utils,
+    Sainsc.KDE,
+    Sainsc.LocalMax,
 ]
 ```
diff --git a/docs/src/examples/ExampleAnalysis.jl b/docs/src/examples/ExampleAnalysis.jl
@@ -2,14 +2,14 @@
 # Example analysis
 
 This is an example workflow demonstrating all the different functionalities the 
-`StereoSSAM.jl` package offers.
+`Sainsc.jl` package offers.
 
 ## General workflow
 
 We start by loading the package and defining the path of some example data.
 =#
 
-using StereoSSAM
+using Sainsc
 
 using ImageTransformations
 using ImageShow
@@ -97,7 +97,7 @@ println("$(length(lm)) local maxima detected")
 #=
 Once we identified the local maxima we can load them for a defined set of genes. 
 [`getlocalmaxima`](@ref) allows you to load the maxima in a variety of output types.
-Have a look at the existing `StereoSSAM.jl` extensions. Here we are going to load them
+Have a look at the existing `Sainsc.jl` extensions. Here we are going to load them
 as `Muon.AnnData` object.
 =#
 
@@ -154,7 +154,7 @@ simshow(imresize(celltype_img; ratio=1 / 45))
 #=
 ## Utils
 
-Some additional useful functions are included in `StereoSSAM.jl`.
+Some additional useful functions are included in `Sainsc.jl`.
 
 ### Cropping & Masking
 

diff --git a/docs/src/examples/ExampleAnalysis.md b/docs/src/examples/ExampleAnalysis.md
@@ -5,14 +5,14 @@ EditURL = "ExampleAnalysis.jl"
 # Example analysis
 
 This is an example workflow demonstrating all the different functionalities the
-`StereoSSAM.jl` package offers.
+`Sainsc.jl` package offers.
 
 ## General workflow
 
 We start by loading the package and defining the path of some example data.
 
 ````julia
-using StereoSSAM
+using Sainsc
 
 using ImageTransformations
 using ImageShow
@@ -129,7 +129,7 @@ println("$(length(lm)) local maxima detected")
 
 Once we identified the local maxima we can load them for a defined set of genes.
 [`getlocalmaxima`](@ref) allows you to load the maxima in a variety of output types.
-Have a look at the existing `StereoSSAM.jl` extensions. Here we are going to load them
+Have a look at the existing `Sainsc.jl` extensions. Here we are going to load them
 as `Muon.AnnData` object.
 
 ````julia
@@ -248,7 +248,7 @@ simshow(imresize(celltype_img; ratio=1 / 45))
 
 ## Utils
 
-Some additional useful functions are included in `StereoSSAM.jl`.
+Some additional useful functions are included in `Sainsc.jl`.
 
 ### Cropping & Masking
 

diff --git a/docs/src/examples/Project.toml b/docs/src/examples/Project.toml
@@ -12,7 +12,7 @@ Muon                 = "446846d7-b4ce-489d-bf74-72da18fe3629"
 OpenCV               = "f878e3a2-a245-4720-8660-60795d644f2a"
 Plots                = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 Printf               = "de0858da-6303-5e67-8744-51eddeeeb8d7"
-StereoSSAM           = "4c4340ea-7f9e-46b4-8512-61f1f6c41a11"
+Sainsc               = "4c4340ea-7f9e-46b4-8512-61f1f6c41a11"
 
 [compat]
 Literate = "2.15.1"
diff --git a/docs/src/index.md b/docs/src/index.md
@@ -1,12 +1,18 @@
-# StereoSSAM.jl
+# Sainsc.jl
 
-TODO general introduction
+`Sainsc.jl` - Segmentation-free analysis of in situ capture data[^1] - is,
+as the name states, a tool to analyse in situ capture-based spatial
+transcriptomics data. Actually, it can also be used to analyse imaging-based datasets.
+For a more thorough background please refer to the
+[original publication](https://TODO)
+or just follow along the provided examplary analysis.
 
-reference to python repo
+A more _batteries included_[^2] version of this package is available in Python/Rust.
+If you are interested have a look at [https://github.com/HiDiHlabs/sainsc](https://github.com/HiDiHlabs/sainsc).
 
 ## Citation
 
-If you use `StereoSSAM.jl` for your research please consider citing
+If you use `Sainsc.jl` for your research please consider citing
 TODO
 
 ## Installation
@@ -15,14 +21,14 @@ The package can be installed with the Julia package manager.
 From the Julia REPL, type `]` to enter the `Pkg` REPL mode and run:
 
 ```
-pkg> add StereoSSAM
+pkg> add Sainsc
 ```
 
 Or, alternatively, via the `Pkg` API:
 
 ```julia
 using Pkg
-Pkg.add("StereoSSAM")
+Pkg.add("Sainsc")
 ```
 
 ## Index
@@ -34,3 +40,6 @@ Pages = [
 ]
 Depth = 3
 ```
+
+[^1]: Some people claim it actually stands for _Stupid Acronyms in Science_
+[^2]: Pun intended
diff --git a/ext/AnnDataExt.jl b/ext/AnnDataExt.jl
@@ -2,9 +2,9 @@ module AnnDataExt
 
 using Muon: AnnData
 
-using StereoSSAM
+using Sainsc
 
-function StereoSSAM.getlocalmaxima(::Type{AnnData}, counts, localmax, kernel; genes=nothing)
+function Sainsc.getlocalmaxima(::Type{AnnData}, counts, localmax, kernel; genes=nothing)
     X, genes, obs = getlocalmaxima(counts, localmax, kernel; genes=genes)
 
     return AnnData(;
@@ -15,7 +15,7 @@ function StereoSSAM.getlocalmaxima(::Type{AnnData}, counts, localmax, kernel; ge
     )
 end
 
-function StereoSSAM.readstereoseqbinned(::Type{AnnData}, file, binsize::Integer)
+function Sainsc.readstereoseqbinned(::Type{AnnData}, file, binsize::Integer)
     X, genes, obs = readstereoseqbinned(file, binsize)
 
     return AnnData(;

diff --git a/ext/AutomaticSingleCellToolboxExt.jl b/ext/AutomaticSingleCellToolboxExt.jl
@@ -4,9 +4,9 @@ using AutomaticSingleCellToolbox: WsObj
 using DataFrames: DataFrame, rename!
 using SparseArrays: nzrange
 
-using StereoSSAM
+using Sainsc
 
-function StereoSSAM.getlocalmaxima(::Type{WsObj}, counts, localmax, kernel; genes=nothing)
+function Sainsc.getlocalmaxima(::Type{WsObj}, counts, localmax, kernel; genes=nothing)
     X, genes, coordinates = getlocalmaxima(counts, localmax, kernel; genes=genes)
 
     coordinates[!, "cell_counts"] = vec(sum(X; dims=1))
@@ -17,7 +17,7 @@ function StereoSSAM.getlocalmaxima(::Type{WsObj}, counts, localmax, kernel; gene
     return WsObj(Dict("raw_dat" => X), coordinates, genes, String[], Dict())
 end
 
-function StereoSSAM.readstereoseqbinned(::Type{WsObj}, file, binsize::Integer)
+function Sainsc.readstereoseqbinned(::Type{WsObj}, file, binsize::Integer)
     X, genes, coordinates = readstereoseqbinned(file, binsize)
 
     coordinates[!, "cell_counts"] = vec(sum(X; dims=1))

diff --git a/ext/CellScopesExt.jl b/ext/CellScopesExt.jl
@@ -3,9 +3,9 @@ module CellScopesExt
 using DataFrames: rename!
 using CellScopes: RawCountObject
 
-using StereoSSAM
+using Sainsc
 
-function StereoSSAM.getlocalmaxima(
+function Sainsc.getlocalmaxima(
     ::Type{RawCountObject}, counts, localmax, kernel; genes=nothing
 )
     mat, genes, coordinates = getlocalmaxima(counts, localmax, kernel; genes=genes)
@@ -15,7 +15,7 @@ function StereoSSAM.getlocalmaxima(
     return RawCountObject(mat, coordinates.cell_name, genes.gene), coordinates
 end
 
-function StereoSSAM.readstereoseqbinned(::Type{RawCountObject}, file, binsize::Integer)
+function Sainsc.readstereoseqbinned(::Type{RawCountObject}, file, binsize::Integer)
     counts, genes, coordinates = readstereoseqbinned(file, binsize)
 
     rename!(coordinates, Dict(:id => "cell_name"))

diff --git a/ext/SingleCellProjectionsExt.jl b/ext/SingleCellProjectionsExt.jl
@@ -2,15 +2,13 @@ module SingleCellProjectionsExt
 
 using SingleCellProjections: DataMatrix
 
-using StereoSSAM
+using Sainsc
 
-function StereoSSAM.getlocalmaxima(
-    ::Type{DataMatrix}, counts, localmax, kernel; genes=nothing
-)
+function Sainsc.getlocalmaxima(::Type{DataMatrix}, counts, localmax, kernel; genes=nothing)
     return DataMatrix(getlocalmaxima(counts, localmax, kernel; genes=genes))
 end
 
-function StereoSSAM.readstereoseqbinned(::Type{DataMatrix}, file, binsize::Integer)
+function Sainsc.readstereoseqbinned(::Type{DataMatrix}, file, binsize::Integer)
     return DataMatrix(readstereoseqbinned(file, binsize))
 end
 

diff --git a/src/IO.jl b/src/IO.jl
@@ -29,6 +29,7 @@ function readGEMfile(file)
     for n in countcol_name
         if n in names(df)
             rename!(df, n => :count)
+            break
         end
     end
-Original file line number
+Diff line change
@@ Expand Up / @@ -29,6 +29,7 @@ function readGEMfile(file) @@
         for n in countcol_name
             if n in names(df)
                 rename!(df, n => :count)
+                break
             end
         end
@@ Expand Down @@