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rockdeme · Sep 1, 2024 · cdeeb2f · cdeeb2f
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diff --git a/...synthetic_data/array_size_benchmark.ipynb → ...synthetic_data/array_size_benchmark.ipynb b/...synthetic_data/array_size_benchmark.ipynb → ...synthetic_data/array_size_benchmark.ipynb
diff --git a/article/I_synthetic_data/bm_functions.py → article/A1_synthetic_data/bm_functions.py b/article/I_synthetic_data/bm_functions.py → article/A1_synthetic_data/bm_functions.py
diff --git a/.../I_synthetic_data/chrysalis_example.ipynb → ...A1_synthetic_data/chrysalis_example.ipynb b/.../I_synthetic_data/chrysalis_example.ipynb → ...A1_synthetic_data/chrysalis_example.ipynb
diff --git a/...thetic_data/contamination_benchmark.ipynb → ...thetic_data/contamination_benchmark.ipynb b/...thetic_data/contamination_benchmark.ipynb → ...thetic_data/contamination_benchmark.ipynb
diff --git a/..._generator/generate_synthetic_datasets.py → ..._generator/generate_synthetic_datasets.py b/..._generator/generate_synthetic_datasets.py → ..._generator/generate_synthetic_datasets.py
diff --git a/...a_generator/generate_truncated_samples.py → ...a_generator/generate_truncated_samples.py b/...a_generator/generate_truncated_samples.py → ...a_generator/generate_truncated_samples.py
diff --git a/...c_data/data_generator/tissue_generator.py → ...c_data/data_generator/tissue_generator.py b/...c_data/data_generator/tissue_generator.py → ...c_data/data_generator/tissue_generator.py
diff --git a/.../I_synthetic_data/data_generator/tools.py → ...A1_synthetic_data/data_generator/tools.py b/.../I_synthetic_data/data_generator/tools.py → ...A1_synthetic_data/data_generator/tools.py
diff --git a/...hetic_data/main_synthetic_benchmark.ipynb → ...hetic_data/main_synthetic_benchmark.ipynb b/...hetic_data/main_synthetic_benchmark.ipynb → ...hetic_data/main_synthetic_benchmark.ipynb
diff --git a/...scripts/array_size_benchmark/chrysalis.py → ...scripts/array_size_benchmark/chrysalis.py b/...scripts/array_size_benchmark/chrysalis.py → ...scripts/array_size_benchmark/chrysalis.py
@@ -6,7 +6,7 @@
 from glob import glob
 import chrysalis as ch
 import matplotlib.pyplot as plt
-from article.I_synthetic_data.bm_functions import get_correlation_df
+from article.A1_synthetic_data.bm_functions import get_correlation_df
 
 
 filepath = 'data/tabula_sapiens_immune_size'

diff --git a/...d_scripts/array_size_benchmark/graphst.py → ...d_scripts/array_size_benchmark/graphst.py b/...d_scripts/array_size_benchmark/graphst.py → ...d_scripts/array_size_benchmark/graphst.py
@@ -7,7 +7,7 @@
 from GraphST import GraphST
 import matplotlib.pyplot as plt
 from sklearn.decomposition import PCA
-from article.I_synthetic_data.bm_functions import get_correlation_df
+from article.A1_synthetic_data.bm_functions import get_correlation_df
 
 
 filepath = '/storage/homefs/pt22a065/chr_data/tabula_sapiens_immune_size'

diff --git a/...d_scripts/array_size_benchmark/mefisto.py → ...d_scripts/array_size_benchmark/mefisto.py b/...d_scripts/array_size_benchmark/mefisto.py → ...d_scripts/array_size_benchmark/mefisto.py
@@ -6,7 +6,7 @@
 import seaborn as sns
 import matplotlib.pyplot as plt
 from mofapy2.run.entry_point import entry_point
-from article.I_synthetic_data.bm_functions import get_correlation_df
+from article.A1_synthetic_data.bm_functions import get_correlation_df
 
 
 filepath = '/storage/homefs/pt22a065/chr_data/tabula_sapiens_immune_size'

diff --git a/...ethod_scripts/array_size_benchmark/nsf.py → ...ethod_scripts/array_size_benchmark/nsf.py b/...ethod_scripts/array_size_benchmark/nsf.py → ...ethod_scripts/array_size_benchmark/nsf.py
@@ -12,7 +12,7 @@
 import matplotlib.pyplot as plt
 from numpy.linalg import LinAlgError
 from tensorflow_probability import math as tm
-from article.I_synthetic_data.bm_functions import get_correlation_df
+from article.A1_synthetic_data.bm_functions import get_correlation_df
 from nsf.utils import preprocess, training, visualize, postprocess, misc
 
 

diff --git a/...d_scripts/array_size_benchmark/stagate.py → ...d_scripts/array_size_benchmark/stagate.py b/...d_scripts/array_size_benchmark/stagate.py → ...d_scripts/array_size_benchmark/stagate.py
@@ -6,7 +6,7 @@
 import seaborn as sns
 import sklearn.neighbors
 import matplotlib.pyplot as plt
-from article.I_synthetic_data.bm_functions import get_correlation_df
+from article.A1_synthetic_data.bm_functions import get_correlation_df
 
 
 filepath = 'data/tabula_sapiens_immune_size'

diff --git a/...ipts/contamination_benchmark/chrysalis.py → ...ipts/contamination_benchmark/chrysalis.py b/...ipts/contamination_benchmark/chrysalis.py → ...ipts/contamination_benchmark/chrysalis.py
@@ -7,7 +7,7 @@
 from glob import glob
 import chrysalis as ch
 import matplotlib.pyplot as plt
-from article.I_synthetic_data.bm_functions import get_correlation_df
+from article.A1_synthetic_data.bm_functions import get_correlation_df
 
 
 filepath = 'data/tabula_sapiens_immune_contamination'

diff --git a/...cripts/contamination_benchmark/graphst.py → ...cripts/contamination_benchmark/graphst.py b/...cripts/contamination_benchmark/graphst.py → ...cripts/contamination_benchmark/graphst.py
@@ -8,7 +8,7 @@
 from GraphST import GraphST
 import matplotlib.pyplot as plt
 from sklearn.decomposition import PCA
-from article.I_synthetic_data.bm_functions import get_correlation_df
+from article.A1_synthetic_data.bm_functions import get_correlation_df
 
 
 filepath = '/storage/homefs/pt22a065/chr_data/tabula_sapiens_immune_contamination'

diff --git a/...cripts/contamination_benchmark/mefisto.py → ...cripts/contamination_benchmark/mefisto.py b/...cripts/contamination_benchmark/mefisto.py → ...cripts/contamination_benchmark/mefisto.py
@@ -7,7 +7,7 @@
 import seaborn as sns
 import matplotlib.pyplot as plt
 from mofapy2.run.entry_point import entry_point
-from article.I_synthetic_data.bm_functions import get_correlation_df
+from article.A1_synthetic_data.bm_functions import get_correlation_df
 
 
 filepath = '/storage/homefs/pt22a065/chr_data/tabula_sapiens_immune_contamination'

diff --git a/...od_scripts/contamination_benchmark/nsf.py → ...od_scripts/contamination_benchmark/nsf.py b/...od_scripts/contamination_benchmark/nsf.py → ...od_scripts/contamination_benchmark/nsf.py
@@ -12,7 +12,7 @@
 import matplotlib.pyplot as plt
 from numpy.linalg import LinAlgError
 from tensorflow_probability import math as tm
-from article.I_synthetic_data.bm_functions import get_correlation_df
+from article.A1_synthetic_data.bm_functions import get_correlation_df
 from nsf.utils import preprocess, training, visualize, postprocess, misc
 
 

diff --git a/...cripts/contamination_benchmark/stagate.py → ...cripts/contamination_benchmark/stagate.py b/...cripts/contamination_benchmark/stagate.py → ...cripts/contamination_benchmark/stagate.py
@@ -7,7 +7,7 @@
 import seaborn as sns
 import sklearn.neighbors
 import matplotlib.pyplot as plt
-from article.I_synthetic_data.bm_functions import get_correlation_df
+from article.A1_synthetic_data.bm_functions import get_correlation_df
 
 
 filepath = 'data/tabula_sapiens_immune_contamination'

diff --git a/...pts/main_synthetic_benchmark/chrysalis.py → ...pts/main_synthetic_benchmark/chrysalis.py b/...pts/main_synthetic_benchmark/chrysalis.py → ...pts/main_synthetic_benchmark/chrysalis.py
@@ -6,7 +6,7 @@
 from glob import glob
 import chrysalis as ch
 import matplotlib.pyplot as plt
-from article.I_synthetic_data.bm_functions import get_correlation_df
+from article.A1_synthetic_data.bm_functions import get_correlation_df
 
 
 filepath = 'data/tabula_sapiens_immune'

diff --git a/...ripts/main_synthetic_benchmark/graphst.py → ...ripts/main_synthetic_benchmark/graphst.py b/...ripts/main_synthetic_benchmark/graphst.py → ...ripts/main_synthetic_benchmark/graphst.py
@@ -7,7 +7,7 @@
 from GraphST import GraphST
 import matplotlib.pyplot as plt
 from sklearn.decomposition import PCA
-from article.I_synthetic_data.bm_functions import get_correlation_df
+from article.A1_synthetic_data.bm_functions import get_correlation_df
 
 
 filepath = 'data/tabula_sapiens_immune'

diff --git a/...ripts/main_synthetic_benchmark/mefisto.py → ...ripts/main_synthetic_benchmark/mefisto.py b/...ripts/main_synthetic_benchmark/mefisto.py → ...ripts/main_synthetic_benchmark/mefisto.py
@@ -6,7 +6,7 @@
 import seaborn as sns
 import matplotlib.pyplot as plt
 from mofapy2.run.entry_point import entry_point
-from article.I_synthetic_data.bm_functions import get_correlation_df
+from article.A1_synthetic_data.bm_functions import get_correlation_df
 
 
 filepath = '/storage/homefs/pt22a065/chr_data/tabula_sapiens_immune'

diff --git a/...d_scripts/main_synthetic_benchmark/nsf.py → ...d_scripts/main_synthetic_benchmark/nsf.py b/...d_scripts/main_synthetic_benchmark/nsf.py → ...d_scripts/main_synthetic_benchmark/nsf.py
@@ -12,7 +12,7 @@
 import matplotlib.pyplot as plt
 from numpy.linalg import LinAlgError
 from tensorflow_probability import math as tm
-from article.I_synthetic_data.bm_functions import get_correlation_df
+from article.A1_synthetic_data.bm_functions import get_correlation_df
 from nsf.utils import preprocess, training, visualize, postprocess, misc
 
 

diff --git a/...ripts/main_synthetic_benchmark/stagate.py → ...ripts/main_synthetic_benchmark/stagate.py b/...ripts/main_synthetic_benchmark/stagate.py → ...ripts/main_synthetic_benchmark/stagate.py
@@ -6,7 +6,7 @@
 import seaborn as sns
 import sklearn.neighbors
 import matplotlib.pyplot as plt
-from article.I_synthetic_data.bm_functions import get_correlation_df
+from article.A1_synthetic_data.bm_functions import get_correlation_df
 
 
 filepath = 'data/tabula_sapiens_immune'

diff --git a/...ction_methods/1_bsp_spatialde_sepal.ipynb → ...ction_methods/1_bsp_spatialde_sepal.ipynb b/...ction_methods/1_bsp_spatialde_sepal.ipynb → ...ction_methods/1_bsp_spatialde_sepal.ipynb
diff --git a/...ymph_node/SVG_detection_methods/2_spark.R → ...ymph_node/SVG_detection_methods/2_spark.R b/...ymph_node/SVG_detection_methods/2_spark.R → ...ymph_node/SVG_detection_methods/2_spark.R
diff --git a/...tection_methods/3_method_comparison.ipynb → ...tection_methods/3_method_comparison.ipynb b/...tection_methods/3_method_comparison.ipynb → ...tection_methods/3_method_comparison.ipynb
diff --git a/..._human_lymph_node/benchmarking/graphst.py → ..._human_lymph_node/benchmarking/graphst.py b/..._human_lymph_node/benchmarking/graphst.py → ..._human_lymph_node/benchmarking/graphst.py
diff --git a/..._human_lymph_node/benchmarking/mefisto.py → ..._human_lymph_node/benchmarking/mefisto.py b/..._human_lymph_node/benchmarking/mefisto.py → ..._human_lymph_node/benchmarking/mefisto.py
diff --git a/...e/II_human_lymph_node/benchmarking/nsf.py → ...e/A2_human_lymph_node/benchmarking/nsf.py b/...e/II_human_lymph_node/benchmarking/nsf.py → ...e/A2_human_lymph_node/benchmarking/nsf.py
diff --git a/...uman_lymph_node/benchmarking/spatialpca.R → ...uman_lymph_node/benchmarking/spatialpca.R b/...uman_lymph_node/benchmarking/spatialpca.R → ...uman_lymph_node/benchmarking/spatialpca.R
diff --git a/..._human_lymph_node/benchmarking/stagate.py → ..._human_lymph_node/benchmarking/stagate.py b/..._human_lymph_node/benchmarking/stagate.py → ..._human_lymph_node/benchmarking/stagate.py
diff --git a/...e/chrysalis_analysis_and_validation.ipynb → ...e/chrysalis_analysis_and_validation.ipynb b/...e/chrysalis_analysis_and_validation.ipynb → ...e/chrysalis_analysis_and_validation.ipynb
diff --git a/article/II_human_lymph_node/morans_i.ipynb → article/A2_human_lymph_node/morans_i.ipynb b/article/II_human_lymph_node/morans_i.ipynb → article/A2_human_lymph_node/morans_i.ipynb
diff --git a/...II_human_breast_cancer/benchmarking.ipynb → ...A3_human_breast_cancer/benchmarking.ipynb b/...II_human_breast_cancer/benchmarking.ipynb → ...A3_human_breast_cancer/benchmarking.ipynb
diff --git a/...man_breast_cancer/benchmarking/graphst.py → ...man_breast_cancer/benchmarking/graphst.py b/...man_breast_cancer/benchmarking/graphst.py → ...man_breast_cancer/benchmarking/graphst.py
diff --git a/...man_breast_cancer/benchmarking/mefisto.py → ...man_breast_cancer/benchmarking/mefisto.py b/...man_breast_cancer/benchmarking/mefisto.py → ...man_breast_cancer/benchmarking/mefisto.py
diff --git a/...I_human_breast_cancer/benchmarking/nsf.py → ...3_human_breast_cancer/benchmarking/nsf.py b/...I_human_breast_cancer/benchmarking/nsf.py → ...3_human_breast_cancer/benchmarking/nsf.py
diff --git a/...n_breast_cancer/benchmarking/spatialpca.R → ...n_breast_cancer/benchmarking/spatialpca.R b/...n_breast_cancer/benchmarking/spatialpca.R → ...n_breast_cancer/benchmarking/spatialpca.R
diff --git a/...man_breast_cancer/benchmarking/stagate.py → ...man_breast_cancer/benchmarking/stagate.py b/...man_breast_cancer/benchmarking/stagate.py → ...man_breast_cancer/benchmarking/stagate.py
diff --git a/...r/chrysalis_analysis_and_validation.ipynb → ...r/chrysalis_analysis_and_validation.ipynb b/...r/chrysalis_analysis_and_validation.ipynb → ...r/chrysalis_analysis_and_validation.ipynb
diff --git a/...y_integration/1_extract_image_tiles.ipynb → ...y_integration/1_extract_image_tiles.ipynb b/...y_integration/1_extract_image_tiles.ipynb → ...y_integration/1_extract_image_tiles.ipynb
diff --git a/...ogy_integration/2_autoencoder_training.py → ...ogy_integration/2_autoencoder_training.py b/...ogy_integration/2_autoencoder_training.py → ...ogy_integration/2_autoencoder_training.py
diff --git a/..._integration/3_integrate_morphology.ipynb → ..._integration/3_integrate_morphology.ipynb b/..._integration/3_integrate_morphology.ipynb → ..._integration/3_integrate_morphology.ipynb
diff --git a/...le/IV_mouse_brain/ff/mouse_brain_ff.ipynb → ...le/A4_mouse_brain/ff/mouse_brain_ff.ipynb b/...le/IV_mouse_brain/ff/mouse_brain_ff.ipynb → ...le/A4_mouse_brain/ff/mouse_brain_ff.ipynb
diff --git a/...se_brain/ff/mouse_brain_integration.ipynb → ...se_brain/ff/mouse_brain_integration.ipynb b/...se_brain/ff/mouse_brain_integration.ipynb → ...se_brain/ff/mouse_brain_integration.ipynb
diff --git a/.../IV_mouse_brain/ffpe/benchmark/graphst.py → .../A4_mouse_brain/ffpe/benchmark/graphst.py b/.../IV_mouse_brain/ffpe/benchmark/graphst.py → .../A4_mouse_brain/ffpe/benchmark/graphst.py
diff --git a/.../IV_mouse_brain/ffpe/benchmark/mefisto.py → .../A4_mouse_brain/ffpe/benchmark/mefisto.py b/.../IV_mouse_brain/ffpe/benchmark/mefisto.py → .../A4_mouse_brain/ffpe/benchmark/mefisto.py
diff --git a/article/IV_mouse_brain/ffpe/benchmark/nsf.py → article/A4_mouse_brain/ffpe/benchmark/nsf.py b/article/IV_mouse_brain/ffpe/benchmark/nsf.py → article/A4_mouse_brain/ffpe/benchmark/nsf.py
diff --git a/.../IV_mouse_brain/ffpe/benchmark/stagate.py → .../A4_mouse_brain/ffpe/benchmark/stagate.py b/.../IV_mouse_brain/ffpe/benchmark/stagate.py → .../A4_mouse_brain/ffpe/benchmark/stagate.py
diff --git a/...le/IV_mouse_brain/ffpe/map_annotations.py → ...le/A4_mouse_brain/ffpe/map_annotations.py b/...le/IV_mouse_brain/ffpe/map_annotations.py → ...le/A4_mouse_brain/ffpe/map_annotations.py
diff --git a/...V_mouse_brain/ffpe/mouse_brain_ffpe.ipynb → ...4_mouse_brain/ffpe/mouse_brain_ffpe.ipynb b/...V_mouse_brain/ffpe/mouse_brain_ffpe.ipynb → ...4_mouse_brain/ffpe/mouse_brain_ffpe.ipynb
diff --git a/...ain/ffpe/mouse_brain_ffpe_benchmark.ipynb → ...ain/ffpe/mouse_brain_ffpe_benchmark.ipynb b/...ain/ffpe/mouse_brain_ffpe_benchmark.ipynb → ...ain/ffpe/mouse_brain_ffpe_benchmark.ipynb
diff --git a/article/V_visium_hd/visium_hd_analysis.ipynb → ...cle/A5_visium_hd/visium_hd_analysis.ipynb b/article/V_visium_hd/visium_hd_analysis.ipynb → ...cle/A5_visium_hd/visium_hd_analysis.ipynb
diff --git a/...VI_slide_seqv2/slide_seqv2_analysis.ipynb → ...A6_slide_seqv2/slide_seqv2_analysis.ipynb b/...VI_slide_seqv2/slide_seqv2_analysis.ipynb → ...A6_slide_seqv2/slide_seqv2_analysis.ipynb
diff --git a/.../VII_stereo_seq/stereo_seq_analysis.ipynb → ...e/A7_stereo_seq/stereo_seq_analysis.ipynb b/.../VII_stereo_seq/stereo_seq_analysis.ipynb → ...e/A7_stereo_seq/stereo_seq_analysis.ipynb