Add Brenner reports; Simplify Brenner setting

manuscript/distances_config.py

@@ -87,3 +87,30 @@ def __init__(self):
         self.RANDOM_SPLIT_BASELINE = False
         self.MARKERS_TO_EXCLUDE = ['MERGED']
         self.REPS = [f'rep{i}' for i in range(1,11)]   
+
+class NIH8DaysDistanceConfig(DistanceConfig):
+    def __init__(self):
+        super().__init__()
+
+        self.INPUT_FOLDERS = ["batch1", "batch2", "batch3"]
+
+        self.EXPERIMENT_TYPE = 'NIH_d8'   
+        self.MARKERS_TO_EXCLUDE = [] 
+        self.CELL_LINES = ['WT']
+        self.BASELINE_CELL_LINE_CONDITION = "WT_Untreated"
+        self.ADD_BATCH_TO_LABEL = True
+        self.ADD_REP_TO_LABEL = True
+
+class NIH8DaysTBK1DistanceConfig(DistanceConfig):
+    def __init__(self):
+        super().__init__()
+
+        self.INPUT_FOLDERS = ["batch1", "batch2", "batch3"]
+
+        self.EXPERIMENT_TYPE = 'NIH_d8'   
+        self.CELL_LINES = ['WT', 'FUSHomozygous','FUSHeterozygous','FUSRevertant']
+        self.CONDITIONS = ['Untreated']
+        self.MARKERS_TO_EXCLUDE = []
+        self.ADD_BATCH_TO_LABEL = True
+        self.ADD_REP_TO_LABEL = True   
+        self.BASELINE_CELL_LINE_CONDITION = "WT_Untreated"

manuscript/embeddings_config.py

@@ -226,3 +226,16 @@ def __init__(self):
         self.MARKERS_TO_EXCLUDE = ['MERGED']
         self.ADD_BATCH_TO_LABEL = True
         self.ADD_REP_TO_LABEL = True
+
+class EmbeddingsNIHDay8DatasetConfig(EmbeddingsConfig):
+    def __init__(self):
+        super().__init__()
+
+        self.INPUT_FOLDERS = [os.path.join(self.PROCESSED_FOLDER_ROOT, "NIH", f) for f in 
+                        ["batch1", "batch2", "batch3"]]
+
+        self.SPLIT_DATA = False
+        self.EXPERIMENT_TYPE = 'NIH_d8'    
+        self.MARKERS_TO_EXCLUDE = None
+        self.ADD_BATCH_TO_LABEL = True
+        self.ADD_REP_TO_LABEL = True

manuscript/manuscript_figures_data_config.py

@@ -90,6 +90,8 @@ def __init__(self):
         # Decide if to show ARI metric on the UMAP
         self.SHOW_ARI = True
         self.ADD_REP_TO_LABEL = False
+
+
 ############################################################
 # Figure 2 
 ############################################################
@@ -185,6 +187,7 @@ def __init__(self):
         self.MARKERS = ['G3BP1', 'DCP1A', 'Phalloidin', 'DAPI']
         self.SHOW_ARI = True
 
+
 ############################################################
 # Figure 3
 ############################################################
@@ -857,4 +860,157 @@ def __init__(self):
         self.INPUT_FOLDERS = ['batch6','batch9']
         self.ADD_BATCH_TO_LABEL = False
 
-        self.CELL_LINES = ['WT','TDP43']
+        self.CELL_LINES = ['WT','TDP43']
+
+
+
+############################################################
+# NIH
+############################################################
+class NeuronsUMAP1B9NIH8DaysFigureConfig(FigureConfig):
+    def __init__(self):
+        super().__init__()
+
+        """UMAP1 of WT untreated
+        """
+
+        # Batches used for model development
+        self.INPUT_FOLDERS = [os.path.join(self.PROCESSED_FOLDER_ROOT, "NIH", f) for f in 
+                        ["batch1","batch2","batch3",]]
+
+        self.EXPERIMENT_TYPE = 'NIH_d8'    
+        self.CELL_LINES = ['WT']
+        self.CONDITIONS = ['Untreated']
+
+        self.MARKERS_TO_EXCLUDE = ['TUJ1', 'TIA1', 'DAPI']
+        # Decide if to show ARI metric on the UMAP
+        self.SHOW_ARI = False
+        self.ADD_REP_TO_LABEL = False
+
+class NIH8DaysDistancesStressFigureConfig(FigureConfig):
+    def __init__(self):
+        super().__init__()
+        """Boxplot of WT stress vs untreated
+        """
+        self.INPUT_FOLDERS =  [os.path.join(self.PROCESSED_FOLDER_ROOT, "NIH", f) for f in 
+                        ["batch2", "batch3"]]
+
+        self.EXPERIMENT_TYPE = 'NIH_d8'
+        self.MARKERS_TO_EXCLUDE = []
+        self.BASELINE_CELL_LINE_CONDITION = "WT_Untreated"
+        self.CELL_LINES_CONDITIONS = ['WT_stress']
+        self.CELL_LINES = ['WT']
+        self.ADD_BATCH_TO_LABEL = True
+        self.ADD_REP_TO_LABEL = True
+
+class NeuronsUMAP0StressNIH8DaysFigureConfig(FigureConfig):
+    def __init__(self):
+        super().__init__()
+        """UMAP0 of single markers - WT untreated vs stress
+        """
+        # Batches used for model development
+        self.INPUT_FOLDERS = [os.path.join(self.PROCESSED_FOLDER_ROOT, "NIH", f) for f in 
+                        ["batch3",]]
+
+        self.EXPERIMENT_TYPE = 'NIH_d8'    
+
+        self.CELL_LINES = ['WT']
+        self.MARKERS_TO_EXCLUDE = []
+
+        # Decide if to show ARI metric on the UMAP
+        self.SHOW_ARI = False
+        self.ADD_REP_TO_LABEL=False
+
+class NIH8DaysDistancesALSFigureConfig(FigureConfig):
+    def __init__(self):
+        """Bubbleplot of WT vs other cell lines
+        """
+        super().__init__()
+        self.INPUT_FOLDERS = [os.path.join(self.PROCESSED_FOLDER_ROOT, "NIH", f) for f in 
+                        ["batch1", "batch2","batch3"]]
+
+        self.EXPERIMENT_TYPE = 'NIH_d8'    
+        self.MARKERS_TO_EXCLUDE = []
+        self.BASELINE_CELL_LINE_CONDITION = "WT_Untreated"
+        self.CONDITIONS = ['Untreated']
+        self.CELL_LINES = ['WT','FUSHomozygous','FUSHeterozygous','FUSRevertant']
+        self.CELL_LINES_CONDITIONS = ['FUSHomozygous_Untreated','FUSHeterozygous_Untreated','FUSRevertant_Untreated']
+        self.ADD_BATCH_TO_LABEL = True
+        self.ADD_REP_TO_LABEL = True
+
+class NIH8DaysUMAP2FigureConfig(FigureConfig):
+    def __init__(self):
+        super().__init__()
+        """UMAP2 multiplex of WT untreated vs stress
+        """
+        # Batches used for model development   
+        self.INPUT_FOLDERS = [os.path.join(self.PROCESSED_FOLDER_ROOT, "NIH", f) for f in 
+                        ["batch3",]]
+        self.EXPERIMENT_TYPE = 'NIH_d8'    
+        self.CELL_LINES = ['WT']
+        self.MARKERS_TO_EXCLUDE = ['TUJ1', 'TIA1']
+        # Decide if to show ARI metric on the UMAP
+        self.SHOW_ARI = True
+        self.ADD_REP_TO_LABEL=False
+
+class NIH8DaysUMAP2ALSD18B2FigureConfig(FigureConfig):
+    def __init__(self):
+        super().__init__()
+        """UMAP2 multiplex of WT untreated vs cell lines
+        """
+        # Batches used for model development   
+        self.INPUT_FOLDERS = [os.path.join(self.PROCESSED_FOLDER_ROOT, "NIH", f) for f in 
+                        ["batch3",]]
+        self.EXPERIMENT_TYPE = 'NIH_d8'   
+        self.MARKERS_TO_EXCLUDE = ['FUS'] 
+        self.CONDITIONS = ['Untreated']
+        # self.CELL_LINES = ['WT','FUSHomozygous','FUSHeterozygous','FUSRevertant']
+        # Decide if to show ARI metric on the UMAP
+        self.SHOW_ARI = True
+        self.ADD_REP_TO_LABEL=False
+
+class NIH8DaysUMAP0ALSFigureConfig(FigureConfig):
+    def __init__(self):
+        super().__init__()
+        self.INPUT_FOLDERS = ["batch1"]
+        self.EXPERIMENT_TYPE = 'NIH_d8'    
+        self.CONDITIONS = ['Untreated']
+        self.MARKERS_TO_EXCLUDE = ['TIA1']
+        # Decide if to show ARI metric on the UMAP
+        self.SHOW_ARI = True
+        self.ADD_REP_TO_LABEL=False
+
+class NIH8DaysUMAP0ALSB9FUSFigureConfig(NIH8DaysUMAP0ALSFigureConfig):
+    def __init__(self):
+        super().__init__()
+        self.INPUT_FOLDERS = ["batch3"]
+        self.CELL_LINES = ['WT','FUSHomozygous','FUSHeterozygous','FUSRevertant']
+        self.MARKERS = ['FUS']
+
+class NIH8DaysUMAP0ALSB9DCP1AFigureConfig(NIH8DaysUMAP0ALSFigureConfig):
+    def __init__(self):
+        super().__init__()
+        self.INPUT_FOLDERS = ["batch1"]
+        self.CELL_LINES = ['WT','FUSHomozygous','FUSHeterozygous','FUSRevertant']
+        self.MARKERS = ['DCP1A']
+
+class NIH8DaysUMAP0ALSB9ANXA11FigureConfig(NIH8DaysUMAP0ALSFigureConfig):
+    def __init__(self):
+        super().__init__()
+        self.INPUT_FOLDERS = ["batch1"]
+        self.CELL_LINES = ['WT','FUSHomozygous','FUSHeterozygous','FUSRevertant']
+        self.MARKERS = ['ANAX11']
+
+class NIH8DaysUMAP0ALSB9CLTCFigureConfig(NIH8DaysUMAP0ALSFigureConfig):
+    def __init__(self):
+        super().__init__()
+        self.INPUT_FOLDERS = ["batch1"]
+        self.CELL_LINES = ['WT','FUSHomozygous','FUSHeterozygous','FUSRevertant']
+        self.MARKERS = ['CLTC']
+
+class NIH8DaysUMAP0ALSB9SQSTM1FigureConfig(NIH8DaysUMAP0ALSFigureConfig):
+    def __init__(self):
+        super().__init__()
+        self.INPUT_FOLDERS = ["batch1"]
+        self.CELL_LINES = ['WT','FUSHomozygous','FUSHeterozygous','FUSRevertant']
+        self.MARKERS = ['SQSTM1']

manuscript/manuscript_plot_config.py

@@ -100,6 +100,7 @@ def __init__(self):
         self.COLOR_MAPPINGS = self.COLOR_MAPPINGS_DOX
         # umap type
         self.UMAP_TYPE = 2
+
 class UMAP0NoMappingPlotConfig(PlotConfig):
     def __init__(self):
         super().__init__()
@@ -241,3 +242,40 @@ def __init__(self):
         super().__init__()
 
         self.COLOR_MAPPINGS_CELL_LINE_CONDITION = self.COLOR_MAPPINGS_ALYSSA
+
+class UMAP1NIH8DaysPlotConfig(PlotConfig):
+    def __init__(self):
+        super().__init__()
+
+        self.ORDERED_MARKER_NAMES = ['DAPI', 'FUS', 'PEX14', 'GM130', 'TDP43', 'Calreticulin', 'Phalloidin', 
+                                    'TOMM20', 'MitoTracker', 'CLTC', 'PURA', 'SNCA', 'KIF5A', 'SQSTM1', 
+                                    'CD41', 'G3BP1', 'FMRP', 'NCL', 'LAMP1', 'PML', 'DCP1A', 'PSD95', 
+                                    'NEMO', 'ANAX11', 'TUJ1', 'P54', 'TIA1']
+
+        # Set the size of the dots
+        self.SIZE = 1
+        self.ALPHA = 1
+        # How labels are shown in legend
+        self.MAP_LABELS_FUNCTION = MapLabelsFunction.MARKERS.name
+        # umap type
+        self.UMAP_TYPE = 1
+        # Colors 
+        self.COLOR_MAPPINGS = self.COLOR_MAPPINGS_NIH
+        self.COLOR_MAPPINGS_MARKERS = self.COLOR_MAPPINGS_NIH
+
+class DistancesNIH8DaysPlotConfig(PlotConfig):
+    ## Bubbleplot
+    def __init__(self):
+        super().__init__()
+
+        self.COLOR_MAPPINGS_CELL_LINE_CONDITION = self.COLOR_MAPPINGS_CONDITION_AND_ALS
+        self.ORDERED_MARKERS = ['GM130','Phalloidin','G3BP1','CLTC','MitoTracker','NCL','KIF5A', 'TOMM20', 'PURA',
+                                'P54','SNCA','ANAX11','FUS','TDP43','PEX14', 'DAPI','PSD95','PML',
+                                'CD41','NEMO','Calreticulin','LAMP1','SQSTM1','DCP1A','FMRP', 'TUJ1', 'TIA1']
+        self.UMAP_TYPE = 2
+        self.COLOR_MAPPINGS_MARKERS = self.COLOR_MAPPINGS_NIH
+
+class NIH8DaysDistanceConfig(DistancesNeuronsStressPlotConfig):
+    def __init__(self):
+        super().__init__()
+        self.COLOR_MAPPINGS_MARKERS = self.COLOR_MAPPINGS_NIH

manuscript/markers_focus_boundries/markers_focus_boundries_NIH.csv

@@ -0,0 +1,28 @@
+,Lower_bound,Upper_bound
+ANAX11,1552.89,12113.94
+DAPI,526.69,5325.03
+SNCA,1875.86,9472.52
+TUJ1,1780.59,27767.24
+DCP1A,3894.81,7877.93
+NEMO,5658.35,22129.45
+CLTC,3112.89,14333.32
+PSD95,3126.78,19160.68
+CD41,1043.58,12823.04
+P54,1912.99,6289.01
+TDP43,2150.63,6611.21
+GM130,4220.58,16063.77
+Phalloidin,5160.47,16337.9
+TOMM20,3055.4,12867.37
+Calreticulin,3176.28,11236.56
+LAMP1,1974.96,7498.93
+FMRP,1576.6,14209.38
+SQSTM1,4203.71,26472.39
+G3BP1,1448.33,8868.45
+KIF5A,2952.11,18337.85
+PEX14,3995.18,12902.94
+PML,2557.14,8454.94
+PURA,1779.85,10983.35
+TIA1,2108.8,12486.45
+FUS,939.45,15847.03
+MitoTracker,2036.35,12753.4
+NCL,454.29,1741.87

manuscript/plot_config.py

@@ -133,3 +133,40 @@ def __init__(self):
         self.COLOR_MAPPINGS_ALYSSA['c9orf72ALSPatients'] = self.COLOR_MAPPINGS_ALYSSA['c9orf72ALSPatients_Untreated']
 
         self.COLOR_MAPPINGS = self.COLOR_MAPPINGS_ALS
+
+        self.COLOR_MAPPINGS_NIH = {
+            'DAPI':{self.MAPPINGS_ALIAS_KEY:'Nucleus', self.MAPPINGS_COLOR_KEY:'#AFBDFF'},
+            'Calreticulin':{self.MAPPINGS_ALIAS_KEY:'ER', self.MAPPINGS_COLOR_KEY:'#4343FE'},
+            'NCL':{self.MAPPINGS_ALIAS_KEY:'Nucleolus', self.MAPPINGS_COLOR_KEY:'#921010'},
+            'TDP43':{self.MAPPINGS_ALIAS_KEY:'TDP-43 granules', self.MAPPINGS_COLOR_KEY:'#12F986'},
+            'TDP43B':{self.MAPPINGS_ALIAS_KEY: 'TDP-43 granules', self.MAPPINGS_COLOR_KEY :'#12F986'},
+            'NONO':{self.MAPPINGS_ALIAS_KEY:'Paraspeckles', self.MAPPINGS_COLOR_KEY:'#66CDAA'},
+            'ANAX11':{self.MAPPINGS_ALIAS_KEY:'ANXA11 granules', self.MAPPINGS_COLOR_KEY:'#18E4CF'},
+            'GM130':{self.MAPPINGS_ALIAS_KEY:'Golgi', self.MAPPINGS_COLOR_KEY:'#168FB2'},
+            'LAMP1':{self.MAPPINGS_ALIAS_KEY:'Lysosome', self.MAPPINGS_COLOR_KEY:'#A80358'},
+            'FUS':{self.MAPPINGS_ALIAS_KEY:'hnRNP complex', self.MAPPINGS_COLOR_KEY:'#9968CB'},
+            'PEX14':{self.MAPPINGS_ALIAS_KEY:'Peroxisome', self.MAPPINGS_COLOR_KEY:'#D257EA'},
+            'DCP1A':{self.MAPPINGS_ALIAS_KEY:'P-Bodies', self.MAPPINGS_COLOR_KEY:'#E6A9EA'},
+            'CD41':{self.MAPPINGS_ALIAS_KEY:'Integrin puncta', self.MAPPINGS_COLOR_KEY:'#F04521'},
+            'SQSTM1':{self.MAPPINGS_ALIAS_KEY:'Autophagosomes', self.MAPPINGS_COLOR_KEY:'#F08F21'},
+            'PML':{self.MAPPINGS_ALIAS_KEY:'PML bodies', self.MAPPINGS_COLOR_KEY:'#F1CBDD'},
+            'SCNA':{self.MAPPINGS_ALIAS_KEY:'Presynapse', self.MAPPINGS_COLOR_KEY:'#FFBF0D'},
+            'SNCA':{self.MAPPINGS_ALIAS_KEY: 'Presynapse', self.MAPPINGS_COLOR_KEY : '#FFBF0D'},
+            'NEMO':{self.MAPPINGS_ALIAS_KEY:'NEMO granules', self.MAPPINGS_COLOR_KEY:'#37378D'},
+            'PSD95':{self.MAPPINGS_ALIAS_KEY:'Postsynapse', self.MAPPINGS_COLOR_KEY:'gray'},
+            'KIF5A':{self.MAPPINGS_ALIAS_KEY:'Transport machinery', self.MAPPINGS_COLOR_KEY:'#DEDB23'},
+            'CLTC':{self.MAPPINGS_ALIAS_KEY:'Coated vesicles', self.MAPPINGS_COLOR_KEY:'#AF8215'},
+            'TOMM20':{self.MAPPINGS_ALIAS_KEY:'MOM', self.MAPPINGS_COLOR_KEY:'#32AC0E'},
+            'MitoTracker':{self.MAPPINGS_ALIAS_KEY:'Mitochondria', self.MAPPINGS_COLOR_KEY:'#898700'},
+            'PURA':{self.MAPPINGS_ALIAS_KEY:'PURA granules', self.MAPPINGS_COLOR_KEY:'#ACE142'},
+            'G3BP1':{self.MAPPINGS_ALIAS_KEY:'Stress granules', self.MAPPINGS_COLOR_KEY:'#F0A3A3'},
+            'Phalloidin':{self.MAPPINGS_ALIAS_KEY:'Cytoskeleton', self.MAPPINGS_COLOR_KEY:'#06A0E9'},
+            'FMRP':{self.MAPPINGS_ALIAS_KEY:'FMRP granules', self.MAPPINGS_COLOR_KEY:'#EF218B'},
+
+            'MERGED':{self.MAPPINGS_ALIAS_KEY:'MERGED', self.MAPPINGS_COLOR_KEY:'gray'},
+            'Map2':{self.MAPPINGS_ALIAS_KEY:'Neuronal marker', self.MAPPINGS_COLOR_KEY:'gray'},
+            # 'TDP43N':{self.MAPPINGS_ALIAS_KEY:'TDP43 granules 2', self.MAPPINGS_COLOR_KEY:'#06A0E9'}
+            'TUJ1':{self.MAPPINGS_ALIAS_KEY:'Microtubule', self.MAPPINGS_COLOR_KEY:'#FF5733'},
+            'P54':{self.MAPPINGS_ALIAS_KEY:'Paraspeckles', self.MAPPINGS_COLOR_KEY:'#66CDAA'},
+            'TIA1':{self.MAPPINGS_ALIAS_KEY:'Stress granule 2', self.MAPPINGS_COLOR_KEY:'#5733FF'},
+        }