diff --git a/viz/js/circle_pack_viz/dist/index_orig.html b/viz/js/circle_pack_viz/dist/index_fold.html similarity index 100% rename from viz/js/circle_pack_viz/dist/index_orig.html rename to viz/js/circle_pack_viz/dist/index_fold.html diff --git a/viz/js/circle_pack_viz/dist/viz.json b/viz/js/circle_pack_viz/dist/viz.json index 3b3a9ad..699e9e9 100644 --- a/viz/js/circle_pack_viz/dist/viz.json +++ b/viz/js/circle_pack_viz/dist/viz.json @@ -2,15 +2,7 @@ { "name": "supercluster_1", "children": [ { -"name": "subcluster_21", "children": [ -{ -"name": "STK40", "size": 1, "studied": "dark"}, - {"name": "STK17B", "size": 1, "studied": "dark"}, - {"name": "TRIB1", "size": 1, "studied": "well"}, - {"name": "TRIB2", "size": 1, "studied": "well"}]} -, - - {"name": "subcluster_8", "children": [ +"name": "subcluster_8", "children": [ { "name": "MAPK6", "size": 1, "studied": "well"}, {"name": "CDC42BPA", "size": 2, "studied": "dark"}, @@ -51,7 +43,15 @@ {"name": "EPHA6", "size": 1, "studied": "well"}, {"name": "EPHA10", "size": 1, "studied": "well"}, {"name": "PTK7", "size": 1, "studied": "well"}, - {"name": "SMG1", "size": 1, "studied": "well"}]}]} + {"name": "SMG1", "size": 1, "studied": "well"}]} +, + + {"name": "subcluster_21", "children": [ +{ +"name": "STK40", "size": 1, "studied": "dark"}, + {"name": "STK17B", "size": 1, "studied": "dark"}, + {"name": "TRIB1", "size": 1, "studied": "well"}, + {"name": "TRIB2", "size": 1, "studied": "well"}]}]} , {"name": "supercluster_2", "children": [ @@ -65,24 +65,6 @@ {"name": "DCLK1", "size": 1, "studied": "well"}]} , - {"name": "subcluster_9", "children": [ -{ -"name": "MARK4", "size": 3, "studied": "dark"}, - {"name": "PLK4", "size": 4, "studied": "well"}, - {"name": "CSNK1A1", "size": 3, "studied": "well"}, - {"name": "DAPK2", "size": 1, "studied": "well"}, - {"name": "EIF2AK4", "size": 1, "studied": "well"}, - {"name": "NEK11", "size": 1, "studied": "dark"}, - {"name": "NEK2", "size": 1, "studied": "well"}, - {"name": "TTBK1", "size": 1, "studied": "dark"}, - {"name": "TTBK2", "size": 1, "studied": "dark"}, - {"name": "CSNK1D", "size": 3, "studied": "well"}, - {"name": "CSNK1E", "size": 3, "studied": "well"}, - {"name": "TSSK2", "size": 1, "studied": "dark"}, - {"name": "NME7", "size": 1, "studied": "well"}, - {"name": "CDK11A", "size": 1, "studied": "dark"}]} -, - {"name": "subcluster_2", "children": [ { "name": "ATR", "size": 1, "studied": "well"}, @@ -207,7 +189,25 @@ {"name": "CLK4", "size": 2, "studied": "dark"}, {"name": "COQ8B", "size": 1, "studied": "dark"}, {"name": "SBK1", "size": 1, "studied": "dark"}, - {"name": "CDKL2", "size": 1, "studied": "dark"}]}]} + {"name": "CDKL2", "size": 1, "studied": "dark"}]} +, + + {"name": "subcluster_9", "children": [ +{ +"name": "MARK4", "size": 3, "studied": "dark"}, + {"name": "PLK4", "size": 4, "studied": "well"}, + {"name": "CSNK1A1", "size": 3, "studied": "well"}, + {"name": "DAPK2", "size": 1, "studied": "well"}, + {"name": "EIF2AK4", "size": 1, "studied": "well"}, + {"name": "NEK11", "size": 1, "studied": "dark"}, + {"name": "NEK2", "size": 1, "studied": "well"}, + {"name": "TTBK1", "size": 1, "studied": "dark"}, + {"name": "TTBK2", "size": 1, "studied": "dark"}, + {"name": "CSNK1D", "size": 3, "studied": "well"}, + {"name": "CSNK1E", "size": 3, "studied": "well"}, + {"name": "TSSK2", "size": 1, "studied": "dark"}, + {"name": "NME7", "size": 1, "studied": "well"}, + {"name": "CDK11A", "size": 1, "studied": "dark"}]}]} , {"name": "supercluster_3", "children": [ @@ -293,7 +293,14 @@ {"name": "supercluster_4", "children": [ { -"name": "subcluster_1", "children": [ +"name": "subcluster_19", "children": [ +{ +"name": "CSNK1G1", "size": 2, "studied": "dark"}, + {"name": "CSNK1G2", "size": 2, "studied": "dark"}, + {"name": "CSNK1G3", "size": 3, "studied": "dark"}]} +, + + {"name": "subcluster_1", "children": [ { "name": "PRKCD", "size": 4, "studied": "well"}, {"name": "PRKCA", "size": 4, "studied": "well"}, @@ -349,13 +356,6 @@ {"name": "CKMT2", "size": 1, "studied": "well"}]} , - {"name": "subcluster_19", "children": [ -{ -"name": "CSNK1G1", "size": 2, "studied": "dark"}, - {"name": "CSNK1G2", "size": 2, "studied": "dark"}, - {"name": "CSNK1G3", "size": 3, "studied": "dark"}]} -, - {"name": "subcluster_16", "children": [ { "name": "HK2", "size": 1, "studied": "well"}, @@ -365,20 +365,7 @@ {"name": "supercluster_5", "children": [ { -"name": "subcluster_15", "children": [ -{ -"name": "RPS6KA4", "size": 3, "studied": "well"}, - {"name": "RPS6KA1", "size": 3, "studied": "well"}, - {"name": "RPS6KA3", "size": 3, "studied": "well"}, - {"name": "RPS6KA2", "size": 1, "studied": "well"}, - {"name": "RPS6KA5", "size": 3, "studied": "well"}, - {"name": "MAPK7", "size": 2, "studied": "well"}, - {"name": "RPS6KA6", "size": 4, "studied": "well"}, - {"name": "DYRK4", "size": 1, "studied": "dark"}, - {"name": "PKMYT1", "size": 2, "studied": "dark"}]} -, - - {"name": "subcluster_13", "children": [ +"name": "subcluster_13", "children": [ { "name": "ARAF", "size": 2, "studied": "well"}, {"name": "MAP2K1", "size": 4, "studied": "well"}, @@ -410,12 +397,33 @@ {"name": "PRKX", "size": 3, "studied": "well"}, {"name": "PGK2", "size": 1, "studied": "well"}, {"name": "MAST4", "size": 1, "studied": "dark"}, - {"name": "AGK", "size": 1, "studied": "well"}]}]} + {"name": "AGK", "size": 1, "studied": "well"}]} +, + + {"name": "subcluster_15", "children": [ +{ +"name": "RPS6KA4", "size": 3, "studied": "well"}, + {"name": "RPS6KA1", "size": 3, "studied": "well"}, + {"name": "RPS6KA3", "size": 3, "studied": "well"}, + {"name": "RPS6KA2", "size": 1, "studied": "well"}, + {"name": "RPS6KA5", "size": 3, "studied": "well"}, + {"name": "MAPK7", "size": 2, "studied": "well"}, + {"name": "RPS6KA6", "size": 4, "studied": "well"}, + {"name": "DYRK4", "size": 1, "studied": "dark"}, + {"name": "PKMYT1", "size": 2, "studied": "dark"}]}]} , {"name": "supercluster_6", "children": [ { -"name": "subcluster_17", "children": [ +"name": "subcluster_23", "children": [ +{ +"name": "NME1", "size": 1, "studied": "well"}, + {"name": "NME4", "size": 1, "studied": "well"}, + {"name": "NME2", "size": 1, "studied": "well"}, + {"name": "NME3", "size": 1, "studied": "well"}]} +, + + {"name": "subcluster_17", "children": [ { "name": "PRKACA", "size": 3, "studied": "well"}, {"name": "CAMKK1", "size": 1, "studied": "dark"}, @@ -434,20 +442,6 @@ {"name": "GRK7", "size": 1, "studied": "well"}]} , - {"name": "subcluster_25", "children": [ -{ -"name": "TRPM7", "size": 1, "studied": "well"}, - {"name": "TRPM6", "size": 1, "studied": "well"}]} -, - - {"name": "subcluster_23", "children": [ -{ -"name": "NME1", "size": 1, "studied": "well"}, - {"name": "NME4", "size": 1, "studied": "well"}, - {"name": "NME2", "size": 1, "studied": "well"}, - {"name": "NME3", "size": 1, "studied": "well"}]} -, - {"name": "subcluster_4", "children": [ { "name": "BRSK1", "size": 1, "studied": "dark"}, @@ -461,17 +455,11 @@ {"name": "SIK3", "size": 4, "studied": "well"}]} , - {"name": "subcluster_18", "children": [ + {"name": "subcluster_10", "children": [ { -"name": "PKM", "size": 1, "studied": "well"}, - {"name": "PFKL", "size": 1, "studied": "well"}, - {"name": "TESK1", "size": 2, "studied": "dark"}, - {"name": "PFKP", "size": 1, "studied": "well"}, - {"name": "PFKM", "size": 1, "studied": "well"}, - {"name": "HIPK1", "size": 1, "studied": "dark"}, - {"name": "DYRK3", "size": 1, "studied": "dark"}, - {"name": "STK33", "size": 1, "studied": "dark"}, - {"name": "DCLK2", "size": 1, "studied": "well"}]} +"name": "PASK", "size": 1, "studied": "well"}, + {"name": "STK16", "size": 4, "studied": "well"}, + {"name": "SNRK", "size": 1, "studied": "well"}]} , {"name": "subcluster_22", "children": [ @@ -496,13 +484,6 @@ {"name": "GALK1", "size": 1, "studied": "well"}]} , - {"name": "subcluster_10", "children": [ -{ -"name": "PASK", "size": 1, "studied": "well"}, - {"name": "STK16", "size": 4, "studied": "well"}, - {"name": "SNRK", "size": 1, "studied": "well"}]} -, - {"name": "subcluster_6", "children": [ { "name": "MYLK", "size": 2, "studied": "well"}, @@ -512,7 +493,26 @@ {"name": "CAMK2A", "size": 1, "studied": "well"}, {"name": "CDKL5", "size": 2, "studied": "dark"}, {"name": "PRKG2", "size": 1, "studied": "well"}, - {"name": "CAMK4", "size": 3, "studied": "well"}]}]} + {"name": "CAMK4", "size": 3, "studied": "well"}]} +, + + {"name": "subcluster_18", "children": [ +{ +"name": "PKM", "size": 1, "studied": "well"}, + {"name": "PFKL", "size": 1, "studied": "well"}, + {"name": "TESK1", "size": 2, "studied": "dark"}, + {"name": "PFKP", "size": 1, "studied": "well"}, + {"name": "PFKM", "size": 1, "studied": "well"}, + {"name": "HIPK1", "size": 1, "studied": "dark"}, + {"name": "DYRK3", "size": 1, "studied": "dark"}, + {"name": "STK33", "size": 1, "studied": "dark"}, + {"name": "DCLK2", "size": 1, "studied": "well"}]} +, + + {"name": "subcluster_25", "children": [ +{ +"name": "TRPM7", "size": 1, "studied": "well"}, + {"name": "TRPM6", "size": 1, "studied": "well"}]}]} , {"name": "supercluster_7", "children": [ @@ -592,6 +592,15 @@ {"name": "CDKL4", "size": 1, "studied": "dark"}]} , + {"name": "subcluster_12", "children": [ +{ +"name": "STK39", "size": 1, "studied": "well"}, + {"name": "WNK1", "size": 1, "studied": "well"}, + {"name": "WNK4", "size": 1, "studied": "well"}, + {"name": "WNK2", "size": 1, "studied": "dark"}, + {"name": "WNK3", "size": 1, "studied": "dark"}]} +, + {"name": "subcluster_5", "children": [ { "name": "BMPR2", "size": 3, "studied": "well"}, @@ -614,16 +623,7 @@ {"name": "ACVR2B", "size": 2, "studied": "well"}, {"name": "VRK2", "size": 1, "studied": "dark"}, {"name": "TSSK1B", "size": 1, "studied": "dark"}, - {"name": "UHMK1", "size": 1, "studied": "well"}]} -, - - {"name": "subcluster_12", "children": [ -{ -"name": "STK39", "size": 1, "studied": "well"}, - {"name": "WNK1", "size": 1, "studied": "well"}, - {"name": "WNK4", "size": 1, "studied": "well"}, - {"name": "WNK2", "size": 1, "studied": "dark"}, - {"name": "WNK3", "size": 1, "studied": "dark"}]}]} + {"name": "UHMK1", "size": 1, "studied": "well"}]}]} , {"name": "supercluster_9", "children": [ diff --git a/viz/js/circle_pack_viz/jsonify_circle_packing.ipynb b/viz/js/circle_pack_viz/jsonify_circle_packing.ipynb index d96ede2..8a2ed8b 100644 --- a/viz/js/circle_pack_viz/jsonify_circle_packing.ipynb +++ b/viz/js/circle_pack_viz/jsonify_circle_packing.ipynb @@ -11,7 +11,15 @@ "cell_type": "code", "execution_count": 1, "metadata": {}, - "outputs": [], + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "ln: ./tools/tools: File exists\n" + ] + } + ], "source": [ "# Important!\n", "# Rather than copy the tools from the src folder of the repository, \n", @@ -62,7 +70,7 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": 3, "metadata": {}, "outputs": [], "source": [ @@ -71,7 +79,7 @@ }, { "cell_type": "code", - "execution_count": 10, + "execution_count": 4, "metadata": {}, "outputs": [ { @@ -209,28 +217,31 @@ ], "source": [ "cluster_dir = '../../../results/networkClusters/'\n", + "# cluster_dir = '../../../results/sensitivityNetworkClusters/'\n", "\n", "louvain_clusters =pd.read_csv(cluster_dir+'louvain_clusters.txt', sep ='\\t').set_index('names')\n", + "# louvain_clusters =pd.read_csv(cluster_dir+'fgr_mapk11_clusts.txt', sep ='\\t').set_index('names')\n", "louvain_clusters.index = pd.Series(louvain_clusters.index).apply(lambda x: hgnc_mapper[x])\n", "display(louvain_clusters.head(5))\n", "\n", "louvain_small_clusters =pd.read_csv(cluster_dir+'louvain_small_clusters.txt', sep ='\\t').set_index('names')\n", + "# louvain_small_clusters =pd.read_csv(cluster_dir+'fgr_mapk11_small_clusts.txt', sep ='\\t').set_index('names')\n", "louvain_small_clusters.index = pd.Series(louvain_small_clusters.index).apply(lambda x: hgnc_mapper[x])\n", "display(louvain_small_clusters.head(5))" ] }, { "cell_type": "code", - "execution_count": 11, + "execution_count": 5, "metadata": {}, "outputs": [ { "data": { "text/plain": [ - "" + "" ] }, - "execution_count": 11, + "execution_count": 5, "metadata": {}, "output_type": "execute_result" }, @@ -263,7 +274,7 @@ }, { "cell_type": "code", - "execution_count": 12, + "execution_count": 6, "metadata": {}, "outputs": [], "source": [ @@ -273,7 +284,7 @@ }, { "cell_type": "code", - "execution_count": 13, + "execution_count": 7, "metadata": { "scrolled": true }, @@ -309,7 +320,7 @@ " 'subcluster_25': 'supercluster_6'}" ] }, - "execution_count": 13, + "execution_count": 7, "metadata": {}, "output_type": "execute_result" } @@ -320,7 +331,7 @@ }, { "cell_type": "code", - "execution_count": 15, + "execution_count": 8, "metadata": {}, "outputs": [ { @@ -393,7 +404,7 @@ "4 LYN PRKCD 3.082207" ] }, - "execution_count": 15, + "execution_count": 8, "metadata": {}, "output_type": "execute_result" } @@ -408,7 +419,7 @@ }, { "cell_type": "code", - "execution_count": 18, + "execution_count": 9, "metadata": {}, "outputs": [ { @@ -487,7 +498,7 @@ "5 MAPKAPK2 VX-702 0.342705 0.743594" ] }, - "execution_count": 18, + "execution_count": 9, "metadata": {}, "output_type": "execute_result" } @@ -520,7 +531,7 @@ }, { "cell_type": "code", - "execution_count": 19, + "execution_count": 10, "metadata": {}, "outputs": [], "source": [ @@ -537,543 +548,24 @@ }, { "cell_type": "code", - "execution_count": 20, + "execution_count": 11, "metadata": {}, "outputs": [ { - "data": { - "text/plain": [ - "{'MST1R': 3,\n", - " 'YES1': 4,\n", - " 'TYRO3': 1,\n", - " 'FGR': 2,\n", - " 'SRC': 4,\n", - " 'ATR': 1,\n", - " 'FLT1': 1,\n", - " 'LYN': 4,\n", - " 'PRKCD': 4,\n", - " 'SYK': 3,\n", - " 'MAP4K1': 4,\n", - " 'PDGFRB': 4,\n", - " 'PIK3CA': 1,\n", - " 'PHKG1': 1,\n", - " 'PHKG2': 3,\n", - " 'PDGFRA': 1,\n", - " 'EIF2AK2': 1,\n", - " 'ARAF': 2,\n", - " 'MAP2K1': 4,\n", - " 'RPS6KA4': 3,\n", - " 'KSR2': 1,\n", - " 'ABL1': 5,\n", - " 'ZAP70': 1,\n", - " 'PTK2B': 4,\n", - " 'MAP2K2': 4,\n", - " 'MAPK1': 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'CKMT2': 1, 'CDKL2': 1, 'GRK1': 1, 'GRK7': 1, 'WNK3': 1, 'HUNK': 1}\n" + ] } ], "source": [ - "sizes" + "print(sizes)" ] }, { "cell_type": "code", - "execution_count": 21, + "execution_count": 12, "metadata": {}, "outputs": [], "source": [ @@ -1084,7 +576,7 @@ }, { "cell_type": "code", - "execution_count": 22, + "execution_count": 13, "metadata": {}, "outputs": [], "source": [ @@ -1093,518 +585,16 @@ }, { "cell_type": "code", - "execution_count": 23, + "execution_count": 14, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ - "[]\n" + "[]\n", + "{'supercluster_1': {'subcluster_8': ['MAPK6', 'CDC42BPA', 'LIMK1', 'LIMK2', 'PAK1', 'KALRN', 'PAK4', 'PAK2', 'HIPK3', 'PAK3', 'PAK6', 'MYLK2', 'MAPK4', 'PAK5', 'MUSK', 'TIE1', 'DDR1', 'BCKDK', 'HUNK'], 'subcluster_7': ['EPHB2', 'RYK', 'EPHB3', 'EPHA4', 'EPHA2', 'EPHA8', 'EPHA3', 'EPHB4', 'EPHB1', 'EPHA1', 'EPHA5', 'EPHA7', 'EPHB6', 'EPHA6', 'EPHA10', 'PTK7', 'SMG1'], 'subcluster_21': ['STK40', 'STK17B', 'TRIB1', 'TRIB2']}, 'supercluster_2': {'subcluster_24': ['MELK', 'MAST3', 'MAP3K21', 'TESK2', 'DCLK1'], 'subcluster_2': ['ATR', 'ABL1', 'DAPK3', 'OBSCN', 'TTN', 'DDR2', 'NTRK1', 'NTRK3', 'WEE1', 'PRKDC', 'ATM', 'LATS1', 'TRIM28', 'BUB1B', 'NEK6', 'CHEK1', 'TLK1', 'CHEK2', 'CASK', 'CSNK2A2', 'MAST2', 'STK36', 'CDK9', 'TLK2', 'PLK1', 'NEK8', 'AURKB', 'CDK4', 'CDK6', 'STK3', 'STK4', 'LATS2', 'BRD2', 'CLK2', 'CLK3', 'CDC7', 'CDK5', 'PBK', 'LRRK1', 'NEK7', 'CSNK2A1', 'LMTK2', 'CDK2', 'BRD4', 'PDXK', 'SLK', 'VRK1', 'VRK3', 'CDK7', 'GAK', 'TAOK1', 'MAST1', 'BUB1', 'SRPK1', 'SRPK2', 'NUAK1', 'RIOK3', 'CDK1', 'STK38', 'TTK', 'AURKA', 'DYRK2', 'CDK13', 'CDK20', 'MAK', 'CDK19', 'CDK8', 'LRRK2', 'RIOK1', 'ICK', 'BMP2K', 'HASPIN', 'DCLK3', 'CDKL3', 'AURKC', 'CDK16', 'CDK3', 'SRPK3', 'CLK1', 'BRD3', 'RIOK2', 'TP53RK', 'CDK12', 'NEK1', 'CDK15', 'CDK14', 'EIF2AK1', 'CDK17', 'CDK18', 'NEK3', 'PEAK1', 'DSTYK', 'SCYL1', 'TNK1', 'PRPF4B', 'SCYL2', 'STK31', 'RIPK4', 'NEK5', 'CAMKV', 'WEE2', 'DCK', 'TEX14', 'STK10', 'STK38L', 'CDK11B', 'PLK3', 'NEK9', 'MASTL', 'PLK2', 'AK2', 'AAK1', 'CIT', 'MARK1', 'PAN3', 'COQ8A', 'ADK', 'AK1', 'FASTKD5', 'CLK4', 'COQ8B', 'SBK1', 'CDKL2'], 'subcluster_9': ['MARK4', 'PLK4', 'CSNK1A1', 'DAPK2', 'EIF2AK4', 'NEK11', 'NEK2', 'TTBK1', 'TTBK2', 'CSNK1D', 'CSNK1E', 'TSSK2', 'NME7', 'CDK11A']}, 'supercluster_3': {'subcluster_11': ['MST1R', 'YES1', 'TYRO3', 'FGR', 'SRC', 'FLT1', 'LYN', 'SYK', 'PDGFRB', 'PIK3CA', 'PDGFRA', 'ZAP70', 'PTK2B', 'PIK3CB', 'BTK', 'MATK', 'TXK', 'MAPK15', 'KDR', 'PTK2', 'TEC', 'TRIO', 'ITK', 'EGFR', 'FLT4', 'FYN', 'MET', 'ERBB4', 'KIT', 'HCK', 'JAK2', 'JAK1', 'LCK', 'PIK3CG', 'TYK2', 'FES', 'JAK3', 'PIP5K1B', 'PIP4K2B', 'PIP5K1A', 'PIP5K1C', 'PIP4K2A', 'PIP4K2C', 'ROCK1', 'ERBB3', 'CSK', 'PIK3C2A', 'ERBB2', 'CSF1R', 'ABL2', 'MERTK', 'TNK2', 'FER', 'ROCK2', 'PIK3CD', 'PI4KA', 'AATK', 'BMX', 'PIM1', 'ROR1', 'PI4K2B', 'BLK', 'PTK6', 'ALK', 'TEK', 'NTRK2', 'LTK', 'FN3KRP', 'FLT3', 'AXL', 'PIKFYVE', 'PDIK1L', 'GUCY2D', 'PRAG1', 'SRMS']}, 'supercluster_4': {'subcluster_19': ['CSNK1G1', 'CSNK1G2', 'CSNK1G3'], 'subcluster_1': ['PRKCD', 'PRKCA', 'PRKCB', 'GSK3B', 'PDPK1', 'PRKCE', 'PRKCG', 'PRKCZ', 'MARK2', 'PRKCQ', 'GUCY2C', 'CHUK', 'PRKCI', 'IKBKB', 'RPS6KB1', 'ILK', 'SGK1', 'MAP3K14', 'PDK2', 'EIF2AK3', 'SGK3', 'RPS6KB2', 'PRKCH', 'PRKD1', 'AKT1', 'GRK2', 'INSR', 'TBK1', 'PDK1', 'GSK3A', 'AKT2', 'IKBKE', 'TRIB3', 'PRKD2', 'MTOR', 'NRBP1', 'CKM', 'GRK5', 'GRK3', 'AKT3', 'PDK3', 'PRKD3', 'ADCK2', 'GRK6', 'TSSK3', 'INSRR', 'STYK1', 'CDC42BPG', 'CDK10', 'NRBP2', 'PDK4', 'CKMT2'], 'subcluster_16': ['HK2', 'KHK', 'HK1']}, 'supercluster_5': {'subcluster_13': ['ARAF', 'MAP2K1', 'KSR2', 'MAP2K2', 'MAPK1', 'MOS', 'MAPK3', 'MARK3', 'TRIM24', 'MKNK1', 'SGK2', 'IGF1R', 'RAF1', 'FGFR1', 'FGFR2', 'FGFR3', 'DAPK1', 'KSR1', 'DMPK', 'PGK1', 'BRAF', 'PIM2', 'MOK', 'HIPK4', 'FRK', 'FGFR4', 'ROS1', 'PRKX', 'PGK2', 'MAST4', 'AGK'], 'subcluster_15': ['RPS6KA4', 'RPS6KA1', 'RPS6KA3', 'RPS6KA2', 'RPS6KA5', 'MAPK7', 'RPS6KA6', 'DYRK4', 'PKMYT1']}, 'supercluster_6': {'subcluster_23': ['NME1', 'NME4', 'NME2', 'NME3'], 'subcluster_17': ['PRKACA', 'CAMKK1', 'DYRK1A', 'SIK2', 'PRKG1', 'SIK1', 'PRKACB', 'PRKACG', 'CAMK1', 'CAMK1G', 'RET', 'CAMK1D', 'NPR1', 'GRK1', 'GRK7'], 'subcluster_4': ['BRSK1', 'STK11', 'STRADA', 'BRSK2', 'STRADB', 'STK24', 'STK25', 'STK26', 'SIK3'], 'subcluster_10': ['PASK', 'STK16', 'SNRK'], 'subcluster_22': ['CHKA', 'CHKB'], 'subcluster_14': ['PHKG1', 'PHKG2', 'EEF2K', 'PRKAA1', 'CAMKK2', 'PRKAA2', 'ULK1', 'PIK3C3', 'PCK2', 'ULK2', 'PIK3R4', 'GALK1'], 'subcluster_6': ['MYLK', 'CAMK2G', 'CAMK2B', 'CAMK2D', 'CAMK2A', 'CDKL5', 'PRKG2', 'CAMK4'], 'subcluster_18': ['PKM', 'PFKL', 'TESK1', 'PFKP', 'PFKM', 'HIPK1', 'DYRK3', 'STK33', 'DCLK2'], 'subcluster_25': ['TRPM7', 'TRPM6']}, 'supercluster_7': {'subcluster_3': ['MAP4K1', 'EIF2AK2', 'DYRK1B', 'IRAK1', 'MAP2K5', 'MAP3K20', 'MAP3K8', 'MAP2K4', 'MAP3K11', 'MAP2K7', 'MAP3K10', 'MAP2K6', 'MAPK14', 'MAP2K3', 'MAPKAPK5', 'MAP3K12', 'MAPK8', 'PKN1', 'MAP3K7', 'MAP3K2', 'MAPK12', 'MAPK13', 'MAPK9', 'MAPK10', 'MAP3K4', 'MAP3K3', 'MAP3K5', 'ERN1', 'PKN2', 'MAPK11', 'RIPK1', 'RIPK2', 'MAP3K1', 'TAOK3', 'CDC42BPB', 'MAP4K5', 'HIPK2', 'IRAK3', 'IRAK4', 'MLKL', 'RIPK3', 'PINK1', 'MAP4K4', 'NLK', 'MKNK2', 'MAP4K2', 'TAOK2', 'IRAK2', 'MAP3K13', 'MAP3K6', 'MAP4K3', 'NEK10', 'MYLK3', 'PRKY', 'MINK1', 'ROR2', 'TNIK', 'MAPKAPK2', 'MAPKAPK3', 'PKN3', 'NRK', 'MAP3K9', 'ADCK1']}, 'supercluster_8': {'subcluster_20': ['CDKL1', 'CDKL4'], 'subcluster_12': ['STK39', 'WNK1', 'WNK4', 'WNK2', 'WNK3'], 'subcluster_5': ['BMPR2', 'AMHR2', 'TGFBR1', 'ACVRL1', 'BMPR1B', 'TGFBR2', 'BMPR1A', 'OXSR1', 'ACVR1', 'NUAK2', 'STK35', 'MYO3A', 'TSSK4', 'ACVR2A', 'SGK196', 'ACVR1B', 'ACVR1C', 'ACVR2B', 'VRK2', 'TSSK1B', 'UHMK1']}, 'supercluster_9': {'subcluster_26': ['IP6K3', 'IP6K1', 'PPIP5K2', 'IP6K2', 'RNASEL', 'PPIP5K1', 'IPMK']}}\n" ] - }, - { - "data": { - "text/plain": [ - "{'supercluster_1': {'subcluster_21': ['STK40', 'STK17B', 'TRIB1', 'TRIB2'],\n", - " 'subcluster_8': 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- " 'AKT3',\n", - " 'PDK3',\n", - " 'PRKD3',\n", - " 'ADCK2',\n", - " 'GRK6',\n", - " 'TSSK3',\n", - " 'INSRR',\n", - " 'STYK1',\n", - " 'CDC42BPG',\n", - " 'CDK10',\n", - " 'NRBP2',\n", - " 'PDK4',\n", - " 'CKMT2'],\n", - " 'subcluster_16': ['HK2', 'KHK', 'HK1'],\n", - " 'subcluster_19': ['CSNK1G1', 'CSNK1G2', 'CSNK1G3']},\n", - " 'supercluster_5': {'subcluster_15': ['RPS6KA4',\n", - " 'RPS6KA1',\n", - " 'RPS6KA3',\n", - " 'RPS6KA2',\n", - " 'RPS6KA5',\n", - " 'MAPK7',\n", - " 'RPS6KA6',\n", - " 'DYRK4',\n", - " 'PKMYT1'],\n", - " 'subcluster_13': ['ARAF',\n", - " 'MAP2K1',\n", - " 'KSR2',\n", - " 'MAP2K2',\n", - " 'MAPK1',\n", - " 'MOS',\n", - " 'MAPK3',\n", - " 'MARK3',\n", - " 'TRIM24',\n", - " 'MKNK1',\n", - " 'SGK2',\n", - " 'IGF1R',\n", - " 'RAF1',\n", - " 'FGFR1',\n", - " 'FGFR2',\n", - " 'FGFR3',\n", - " 'DAPK1',\n", - " 'KSR1',\n", - " 'DMPK',\n", - " 'PGK1',\n", - " 'BRAF',\n", - " 'PIM2',\n", - " 'MOK',\n", - " 'HIPK4',\n", - " 'FRK',\n", - " 'FGFR4',\n", - " 'ROS1',\n", - " 'PRKX',\n", - " 'PGK2',\n", - " 'MAST4',\n", - " 'AGK']},\n", - " 'supercluster_6': {'subcluster_6': ['MYLK',\n", - " 'CAMK2G',\n", - " 'CAMK2B',\n", - " 'CAMK2D',\n", - " 'CAMK2A',\n", - " 'CDKL5',\n", - " 'PRKG2',\n", - " 'CAMK4'],\n", - " 'subcluster_18': ['PKM',\n", - " 'PFKL',\n", - " 'TESK1',\n", - " 'PFKP',\n", - " 'PFKM',\n", - " 'HIPK1',\n", - " 'DYRK3',\n", - " 'STK33',\n", - " 'DCLK2'],\n", - " 'subcluster_25': ['TRPM7', 'TRPM6'],\n", - " 'subcluster_4': ['BRSK1',\n", - " 'STK11',\n", - " 'STRADA',\n", - " 'BRSK2',\n", - " 'STRADB',\n", - " 'STK24',\n", - " 'STK25',\n", - " 'STK26',\n", - " 'SIK3'],\n", - " 'subcluster_10': ['PASK', 'STK16', 'SNRK'],\n", - " 'subcluster_23': ['NME1', 'NME4', 'NME2', 'NME3'],\n", - " 'subcluster_17': ['PRKACA',\n", - " 'CAMKK1',\n", - " 'DYRK1A',\n", - " 'SIK2',\n", - " 'PRKG1',\n", - " 'SIK1',\n", - " 'PRKACB',\n", - " 'PRKACG',\n", - " 'CAMK1',\n", - " 'CAMK1G',\n", - " 'RET',\n", - " 'CAMK1D',\n", - " 'NPR1',\n", - " 'GRK1',\n", - " 'GRK7'],\n", - " 'subcluster_22': ['CHKA', 'CHKB'],\n", - " 'subcluster_14': ['PHKG1',\n", - " 'PHKG2',\n", - " 'EEF2K',\n", - " 'PRKAA1',\n", - " 'CAMKK2',\n", - " 'PRKAA2',\n", - " 'ULK1',\n", - " 'PIK3C3',\n", - " 'PCK2',\n", - " 'ULK2',\n", - " 'PIK3R4',\n", - " 'GALK1']},\n", - " 'supercluster_7': {'subcluster_3': ['MAP4K1',\n", - " 'EIF2AK2',\n", - " 'DYRK1B',\n", - " 'IRAK1',\n", - " 'MAP2K5',\n", - " 'MAP3K20',\n", - " 'MAP3K8',\n", - " 'MAP2K4',\n", - " 'MAP3K11',\n", - " 'MAP2K7',\n", - " 'MAP3K10',\n", - " 'MAP2K6',\n", - " 'MAPK14',\n", - " 'MAP2K3',\n", - " 'MAPKAPK5',\n", - " 'MAP3K12',\n", - " 'MAPK8',\n", - " 'PKN1',\n", - " 'MAP3K7',\n", - " 'MAP3K2',\n", - " 'MAPK12',\n", - " 'MAPK13',\n", - " 'MAPK9',\n", - " 'MAPK10',\n", - " 'MAP3K4',\n", - " 'MAP3K3',\n", - " 'MAP3K5',\n", - " 'ERN1',\n", - " 'PKN2',\n", - " 'MAPK11',\n", - " 'RIPK1',\n", - " 'RIPK2',\n", - " 'MAP3K1',\n", - " 'TAOK3',\n", - " 'CDC42BPB',\n", - " 'MAP4K5',\n", - " 'HIPK2',\n", - " 'IRAK3',\n", - " 'IRAK4',\n", - " 'MLKL',\n", - " 'RIPK3',\n", - " 'PINK1',\n", - " 'MAP4K4',\n", - " 'NLK',\n", - " 'MKNK2',\n", - " 'MAP4K2',\n", - " 'TAOK2',\n", - " 'IRAK2',\n", - " 'MAP3K13',\n", - " 'MAP3K6',\n", - " 'MAP4K3',\n", - " 'NEK10',\n", - " 'MYLK3',\n", - " 'PRKY',\n", - " 'MINK1',\n", - " 'ROR2',\n", - " 'TNIK',\n", - " 'MAPKAPK2',\n", - " 'MAPKAPK3',\n", - " 'PKN3',\n", - " 'NRK',\n", - " 'MAP3K9',\n", - " 'ADCK1']},\n", - " 'supercluster_8': {'subcluster_20': ['CDKL1', 'CDKL4'],\n", - " 'subcluster_12': ['STK39', 'WNK1', 'WNK4', 'WNK2', 'WNK3'],\n", - " 'subcluster_5': ['BMPR2',\n", - " 'AMHR2',\n", - " 'TGFBR1',\n", - " 'ACVRL1',\n", - " 'BMPR1B',\n", - " 'TGFBR2',\n", - " 'BMPR1A',\n", - " 'OXSR1',\n", - " 'ACVR1',\n", - " 'NUAK2',\n", - " 'STK35',\n", - " 'MYO3A',\n", - " 'TSSK4',\n", - " 'ACVR2A',\n", - " 'SGK196',\n", - " 'ACVR1B',\n", - " 'ACVR1C',\n", - " 'ACVR2B',\n", - " 'VRK2',\n", - " 'TSSK1B',\n", - " 'UHMK1']},\n", - " 'supercluster_9': {'subcluster_26': ['IP6K3',\n", - " 'IP6K1',\n", - " 'PPIP5K2',\n", - " 'IP6K2',\n", - " 'RNASEL',\n", - " 'PPIP5K1',\n", - " 'IPMK']}}" - ] - }, - "execution_count": 23, - "metadata": {}, - "output_type": "execute_result" } ], "source": [ @@ -1622,12 +612,12 @@ "missing_parents = {x:kin_arr[kin_parents==x].tolist() for x in missing_parents}\n", "\n", "# display \n", - "parents_plus_children" + "print(parents_plus_children)" ] }, { "cell_type": "code", - "execution_count": 24, + "execution_count": 15, "metadata": {}, "outputs": [], "source": [ @@ -1645,7 +635,7 @@ }, { "cell_type": "code", - "execution_count": 28, + "execution_count": 16, "metadata": {}, "outputs": [ { @@ -1749,7 +739,7 @@ "4 Q96L96 AlphaK1 " ] }, - "execution_count": 28, + "execution_count": 16, "metadata": {}, "output_type": "execute_result" } @@ -1761,7 +751,7 @@ }, { "cell_type": "code", - "execution_count": 29, + "execution_count": 17, "metadata": {}, "outputs": [ { @@ -1788,13 +778,13 @@ }, { "cell_type": "code", - "execution_count": 30, + "execution_count": 18, "metadata": {}, "outputs": [], "source": [ - "fold_dict = pd.read_csv('./dist/viz_fold.csv', index_col=0)\n", - "fold_dict['fold_change'] = fold_dict['fold_change'].apply(lambda x: 0.0 if x == np.nan else x)\n", - "fold_dict = fold_dict.to_dict()['fold_change']" + "# fold_dict = pd.read_csv('./dist/viz_fold.csv', index_col=0)\n", + "# fold_dict['fold_change'] = fold_dict['fold_change'].apply(lambda x: 0.0 if x == np.nan else x)\n", + "# fold_dict = fold_dict.to_dict()['fold_change']" ] }, { @@ -1806,7 +796,7 @@ }, { "cell_type": "code", - "execution_count": 31, + "execution_count": 20, "metadata": {}, "outputs": [], "source": [ @@ -1819,12 +809,26 @@ " \"children\":[\n", " {\"name\":str(k),\n", " \"size\":int(sizes[k]),\n", - " \"studied\":dark_dict[k],\n", - " \"fold\":fold_dict[k]}\n", + " \"studied\":dark_dict[k]}\n", " for k in kinases]}\n", " for child, kinases in children.items()]} \n", " for parent, children in parents_plus_children.items()]}\n", "\n", + "# fold support \n", + "# json_out = {\"name\":\"viz\",\n", + "# \"children\":[\n", + "# {\"name\":str(parent), \n", + "# \"children\":[\n", + "# {\"name\":str(child), \n", + "# \"children\":[\n", + "# {\"name\":str(k),\n", + "# \"size\":int(sizes[k]),\n", + "# \"studied\":dark_dict[k],\n", + "# \"fold\":fold_dict[k]}\n", + "# for k in kinases]}\n", + "# for child, kinases in children.items()]} \n", + "# for parent, children in parents_plus_children.items()]}\n", + "\n", "# extra json\n", "missing_json = [\n", " {\"name\":str(parent),\n", @@ -1839,7 +843,7 @@ }, { "cell_type": "code", - "execution_count": 32, + "execution_count": 21, "metadata": {}, "outputs": [], "source": [ @@ -1850,7 +854,7 @@ }, { "cell_type": "code", - "execution_count": 33, + "execution_count": 22, "metadata": {}, "outputs": [], "source": [