Merge pull request #8 from CostaLab/dev

test files updated to reflect annData changes

Author: ruthvik07

docs/requirements.txt

@@ -8,3 +8,4 @@ gprofiler-official
 sankeyflow
 nbformat
 anndata
+scanpy

docs/source/notebooks/Human_Myelofibrosis.ipynb

@@ -4204,7 +4204,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": null,
    "id": "0b02bd3f",
    "metadata": {},
    "outputs": [
@@ -4220,12 +4220,12 @@
     }
    ],
    "source": [
-    "ctpl.plot_volcane(adata.uns['pycrosstalker']['results']['stats']['ischemic_x_myogenic'], \"fisher\", 0.05, 2, annot=False, title=\"Volcano Plot for Ischemic vs Myogenic on Fisher Filtered Data\")"
+    "ctpl.plot_volcane(adata.uns['pycrosstalker']['results']['stats']['ischemic_x_myogenic'], \"fisher\", p_threshold=0.05, fc_threshold=2, annot=False, title=\"Volcano Plot for Ischemic vs Myogenic on Fisher Filtered Data\")"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": null,
    "id": "040329fe",
    "metadata": {},
    "outputs": [
@@ -4241,7 +4241,7 @@
     }
    ],
    "source": [
-    "ctpl.plot_volcane(adata.uns['pycrosstalker']['results']['stats']['ischemic_x_myogenic:MannU'], \"mannwhitneyu\", 0.05, 2, annot = False, title=\"Volcano Plot for Ischemic vs Myogenic on Mann-Whitney U Filtered Data\")"
+    "ctpl.plot_volcane(adata.uns['pycrosstalker']['results']['stats']['ischemic_x_myogenic:MannU'], \"mannwhitneyu\", p_threshold=0.05, fc_threshold=2, annot = False, title=\"Volcano Plot for Ischemic vs Myogenic on Mann-Whitney U Filtered Data\")"
    ]
   },
   {

docs/source/notebooks/Human_Myocardial_Infarction.ipynb

@@ -628,18 +628,19 @@ def mannwhitneyu_test_cci(annData, measure, out_path, comparison=None):
                 c = data['tables'][ctr_name].loc[data['tables'][ctr_name]['cellpair'] == cellpair, ['allpair', measure]]
                 e = data['tables'][exp_name].loc[data['tables'][exp_name]['cellpair'] == cellpair, ['allpair', measure]]
 
-                merged = pd.merge(c, e, on='allpair', how='outer').fillna(0)
-                
-                stat, p_value = mannwhitneyu(merged[measure + '_x'], merged[measure + '_y'], alternative='two-sided')
-                eps = 1e-6
-                lfc = np.log2((merged[measure + '_y'].mean() + eps) / (merged[measure + '_x'].mean() + eps)) if merged[measure + '_x'].mean() > 0 else np.nan
-
-                results.append({
-                    'cellpair': cellpair,
-                    'statistic': stat,
-                    'p_value': p_value,
-                    'lfc': lfc
-                })
+                #merged = pd.merge(c, e, on='allpair', how='outer').fillna(0)
+                merged = pd.merge(c, e, on='allpair', how='inner')
+                if len(merged) > 0:
+                    stat, p_value = mannwhitneyu(merged[measure + '_x'], merged[measure + '_y'], alternative='two-sided')
+                    eps = 1e-6
+                    lfc = np.log2((merged[measure + '_y'].mean() + eps) / (merged[measure + '_x'].mean() + eps)) if merged[measure + '_x'].mean() > 0 else np.nan
+
+                    results.append({
+                        'cellpair': cellpair,
+                        'statistic': stat,
+                        'p_value': p_value,
+                        'lfc': lfc
+                    })
 
             data['stats'][f'{exp_name}_x_{ctr_name}:MannU'] = pd.DataFrame(results)
 

poetry.lock

@@ -25,7 +25,8 @@ dependencies = [
     "plotly>=6.0.1",
     "sankeyflow>=0.4.1",
     "gprofiler-official==1.0.0",
-    "anndata (>=0.12.2,<0.13.0)"
+    "anndata (>=0.12.2,<0.13.0)",
+    "scanpy (>=1.11.4,<2.0.0)"
 ]
 
 [build-system]

pycrosstalker/tools/utils.py

@@ -495,6 +495,28 @@ kiwisolver==1.4.5 ; python_version >= "3.11" \
 legacy-api-wrap==1.4.1 ; python_version >= "3.11" \
     --hash=sha256:8ba214242e836cebfd3b64c1a1653fce955abb0f9e4c7dffb51f2ad014def0eb \
     --hash=sha256:9c40d67aa8312fec8763e87cbf28fea4b67710c79ca7a18137b573d150f3b2b4
+llvmlite==0.45.1 ; python_version >= "3.11" \
+    --hash=sha256:02a164db2d79088bbd6e0d9633b4fe4021d6379d7e4ac7cc85ed5f44b06a30c5 \
+    --hash=sha256:080e6f8d0778a8239cd47686d402cb66eb165e421efa9391366a9b7e5810a38b \
+    --hash=sha256:09430bb9d0bb58fc45a45a57c7eae912850bedc095cd0810a57de109c69e1c32 \
+    --hash=sha256:1a53f4b74ee9fd30cb3d27d904dadece67a7575198bd80e687ee76474620735f \
+    --hash=sha256:1b1af0c910af0978aa55fa4f60bbb3e9f39b41e97c2a6d94d199897be62ba07a \
+    --hash=sha256:28e763aba92fe9c72296911e040231d486447c01d4f90027c8e893d89d49b20e \
+    --hash=sha256:2f3377a6db40f563058c9515dedcc8a3e562d8693a106a28f2ddccf2c8fcf6ca \
+    --hash=sha256:3aa3dfceda4219ae39cf18806c60eeb518c1680ff834b8b311bd784160b9ce40 \
+    --hash=sha256:3adc2355694d6a6fbcc024d59bb756677e7de506037c878022d7b877e7613a36 \
+    --hash=sha256:4edb62e685867799e336723cb9787ec6598d51d0b1ed9af0f38e692aa757e898 \
+    --hash=sha256:57c48bf2e1083eedbc9406fb83c4e6483017879714916fe8be8a72a9672c995a \
+    --hash=sha256:5b3796b1b1e1c14dcae34285d2f4ea488402fbd2c400ccf7137603ca3800864f \
+    --hash=sha256:60f92868d5d3af30b4239b50e1717cb4e4e54f6ac1c361a27903b318d0f07f42 \
+    --hash=sha256:779e2f2ceefef0f4368548685f0b4adde34e5f4b457e90391f570a10b348d433 \
+    --hash=sha256:98baab513e19beb210f1ef39066288784839a44cd504e24fff5d17f1b3cf0860 \
+    --hash=sha256:9e6c9949baf25d9aa9cd7cf0f6d011b9ca660dd17f5ba2b23bdbdb77cc86b116 \
+    --hash=sha256:c9f3cadee1630ce4ac18ea38adebf2a4f57a89bd2740ce83746876797f6e0bfb \
+    --hash=sha256:d9ea9e6f17569a4253515cc01dade70aba536476e3d750b2e18d81d7e670eb15 \
+    --hash=sha256:f2d47f34e4029e6df3395de34cc1c66440a8d72712993a6e6168db228686711b \
+    --hash=sha256:f7319e5f9f90720578a7f56fbc805bdfb4bc071b507c7611f170d631c3c0f1e0 \
+    --hash=sha256:f9c272682d91e0d57f2a76c6d9ebdfccc603a01828cdbe3d15273bdca0c3363a
 matplotlib==3.9.2 ; python_version >= "3.11" \
     --hash=sha256:039082812cacd6c6bec8e17a9c1e6baca230d4116d522e81e1f63a74d01d2e21 \
     --hash=sha256:03ba9c1299c920964e8d3857ba27173b4dbb51ca4bab47ffc2c2ba0eb5e2cbc5 \
@@ -548,6 +570,28 @@ natsort==8.4.0 ; python_version >= "3.11" \
 networkx==3.3 ; python_version >= "3.11" \
     --hash=sha256:0c127d8b2f4865f59ae9cb8aafcd60b5c70f3241ebd66f7defad7c4ab90126c9 \
     --hash=sha256:28575580c6ebdaf4505b22c6256a2b9de86b316dc63ba9e93abde3d78dfdbcf2
+numba==0.62.1 ; python_version >= "3.11" \
+    --hash=sha256:03de6d691d6b6e2b76660ba0f38f37b81ece8b2cc524a62f2a0cfae2bfb6f9da \
+    --hash=sha256:14432af305ea68627a084cd702124fd5d0c1f5b8a413b05f4e14757202d1cf6c \
+    --hash=sha256:1b743b32f8fa5fff22e19c2e906db2f0a340782caf024477b97801b918cf0494 \
+    --hash=sha256:44a1412095534a26fb5da2717bc755b57da5f3053965128fe3dc286652cc6a92 \
+    --hash=sha256:44e3aa6228039992f058f5ebfcfd372c83798e9464297bdad8cc79febcf7891e \
+    --hash=sha256:57cbddc53b9ee02830b828a8428757f5c218831ccc96490a314ef569d8342b7b \
+    --hash=sha256:604059730c637c7885386521bb1b0ddcbc91fd56131a6dcc54163d6f1804c872 \
+    --hash=sha256:6ef84d0ac19f1bf80431347b6f4ce3c39b7ec13f48f233a48c01e2ec06ecbc59 \
+    --hash=sha256:728f91a874192df22d74e3fd42c12900b7ce7190b1aad3574c6c61b08313e4c5 \
+    --hash=sha256:7b774242aa890e34c21200a1fc62e5b5757d5286267e71103257f4e2af0d5161 \
+    --hash=sha256:8c9460b9e936c5bd2f0570e20a0a5909ee6e8b694fd958b210e3bde3a6dba2d7 \
+    --hash=sha256:90fa21b0142bcf08ad8e32a97d25d0b84b1e921bc9423f8dda07d3652860eef6 \
+    --hash=sha256:9315cc5e441300e0ca07c828a627d92a6802bcbf27c5487f31ae73783c58da53 \
+    --hash=sha256:a323df9d36a0da1ca9c592a6baaddd0176d9f417ef49a65bb81951dce69d941a \
+    --hash=sha256:b72489ba8411cc9fdcaa2458d8f7677751e94f0109eeb53e5becfdc818c64afb \
+    --hash=sha256:bbf3f88b461514287df66bc8d0307e949b09f2b6f67da92265094e8fa1282dd8 \
+    --hash=sha256:d6c540880170bee817011757dc9049dba5a29db0c09b4d2349295991fe3ee55f \
+    --hash=sha256:e1e1f4781d3f9f7c23f16eb04e76ca10b5a3516e959634bd226fc48d5d8e7a0a \
+    --hash=sha256:f180922adf159ae36c2fe79fb94ffaa74cf5cb3688cb72dba0a904b91e978507 \
+    --hash=sha256:f41834909d411b4b8d1c68f745144136f21416547009c1e860cc2098754b4ca7 \
+    --hash=sha256:f43e24b057714e480fe44bc6031de499e7cf8150c63eb461192caa6cc8530bc8
 numcodecs==0.16.3 ; python_version >= "3.11" \
     --hash=sha256:010d628c95be1214536fb22c0df4ced58da954b404b1fcb25ddebf64e4a3f7f3 \
     --hash=sha256:12f43fa4a347d1dba775c4506a1c9b15b90144c258433b81f79f1c1b1a990db5 \
@@ -725,6 +769,9 @@ plotly==6.0.1 ; python_version >= "3.11" \
 plotnine==0.13.6 ; python_version >= "3.11" \
     --hash=sha256:3c8c8f958c295345140230ea29803488f83aba9b5a8d0b1b2eb3eaefbf0a06b8 \
     --hash=sha256:4acc1af29fa4e91e726b67d49277e8368f62e1c817f01bf14ecd8ca5e83bfaea
+pynndescent==0.5.13 ; python_version >= "3.11" \
+    --hash=sha256:69aabb8f394bc631b6ac475a1c7f3994c54adf3f51cd63b2730fefba5771b949 \
+    --hash=sha256:d74254c0ee0a1eeec84597d5fe89fedcf778593eeabe32c2f97412934a9800fb
 pyparsing==3.1.2 ; python_version >= "3.11" \
     --hash=sha256:a1bac0ce561155ecc3ed78ca94d3c9378656ad4c94c1270de543f621420f94ad \
     --hash=sha256:f9db75911801ed778fe61bb643079ff86601aca99fcae6345aa67292038fb742
@@ -814,6 +861,9 @@ requests==2.32.3 ; python_version >= "3.11" \
 sankeyflow==0.4.1 ; python_version >= "3.11" \
     --hash=sha256:268dae6e1fea3207034eda628d7927c8225f72879ad968d03afde132e600e918 \
     --hash=sha256:f9fea7720300b4d73cbb18b9e6b507a4d69f25ea5bf8b2fb7b7d47ee222a58c0
+scanpy==1.11.4 ; python_version >= "3.11" \
+    --hash=sha256:333189ecac9c7009bf55d416ee2e272e1c490d54c719478f7b4dd1fc294d2f95 \
+    --hash=sha256:f4ab68ab89e97e88a4faed07b1bc51533fb2e67f797a65a4683591910abfab95
 scikit-learn==1.5.1 ; python_version >= "3.11" \
     --hash=sha256:0828673c5b520e879f2af6a9e99eee0eefea69a2188be1ca68a6121b809055c1 \
     --hash=sha256:0ea5d40c0e3951df445721927448755d3fe1d80833b0b7308ebff5d2a45e6414 \
@@ -865,34 +915,43 @@ scipy==1.14.0 ; python_version >= "3.11" \
 seaborn==0.13.2 ; python_version >= "3.11" \
     --hash=sha256:636f8336facf092165e27924f223d3c62ca560b1f2bb5dff7ab7fad265361987 \
     --hash=sha256:93e60a40988f4d65e9f4885df477e2fdaff6b73a9ded434c1ab356dd57eefff7
+session-info2==0.2.3 ; python_version >= "3.11" \
+    --hash=sha256:6d16e3c6bb72ea52e589da4d722d24798aa3511c34ab8446a131d655cba2e2c9 \
+    --hash=sha256:f211d9930f73b485b727b6c4d8b964fa1b634351b3079393738f42be9b4c7f5e
 six==1.16.0 ; python_version >= "3.11" \
     --hash=sha256:1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926 \
     --hash=sha256:8abb2f1d86890a2dfb989f9a77cfcfd3e47c2a354b01111771326f8aa26e0254
-statsmodels==0.14.2 ; python_version >= "3.11" \
-    --hash=sha256:0e46e9d59293c1af4cc1f4e5248f17e7e7bc596bfce44d327c789ac27f09111b \
-    --hash=sha256:10f2b7611a61adb7d596a6d239abdf1a4d5492b931b00d5ed23d32844d40e48e \
-    --hash=sha256:201c3d00929c4a67cda1fe05b098c8dcf1b1eeefa88e80a8f963a844801ed59f \
-    --hash=sha256:29c78a7601fdae1aa32104c5ebff2e0b72c26f33e870e2f94ab1bcfd927ece9b \
-    --hash=sha256:4864a1c4615c5ea5f2e3b078a75bdedc90dd9da210a37e0738e064b419eccee2 \
-    --hash=sha256:50fcb633987779e795142f51ba49fb27648d46e8a1382b32ebe8e503aaabaa9e \
-    --hash=sha256:55d1742778400ae67acb04b50a2c7f5804182f8a874bd09ca397d69ed159a751 \
-    --hash=sha256:5827a12e3ede2b98a784476d61d6bec43011fedb64aa815f2098e0573bece257 \
-    --hash=sha256:7a91f6c4943de13e3ce2e20ee3b5d26d02bd42300616a421becd53756f5deb37 \
-    --hash=sha256:876794068abfaeed41df71b7887000031ecf44fbfa6b50d53ccb12ebb4ab747a \
-    --hash=sha256:8875823bdd41806dc853333cc4e1b7ef9481bad2380a999e66ea42382cf2178d \
-    --hash=sha256:890550147ad3a81cda24f0ba1a5c4021adc1601080bd00e191ae7cd6feecd6ad \
-    --hash=sha256:8e004cfad0e46ce73fe3f3812010c746f0d4cfd48e307b45c14e9e360f3d2510 \
-    --hash=sha256:90fd2f0110b73fc3fa5a2f21c3ca99b0e22285cccf38e56b5b8fd8ce28791b0f \
-    --hash=sha256:9edefa4ce08e40bc1d67d2f79bc686ee5e238e801312b5a029ee7786448c389a \
-    --hash=sha256:a87ef21fadb445b650f327340dde703f13aec1540f3d497afb66324499dea97a \
-    --hash=sha256:ac780ad9ff552773798829a0b9c46820b0faa10e6454891f5e49a845123758ab \
-    --hash=sha256:afbd92410e0df06f3d8c4e7c0e2e71f63f4969531f280fb66059e2ecdb6e0415 \
-    --hash=sha256:c254c66142f1167b4c7d031cf8db55294cc62ff3280e090fc45bd10a7f5fd029 \
-    --hash=sha256:df5d6f95c46f0341da6c79ee7617e025bf2b371e190a8e60af1ae9cabbdb7a97 \
-    --hash=sha256:eb0ba1ad3627705f5ae20af6b2982f500546d43892543b36c7bca3e2f87105e7 \
-    --hash=sha256:f36494df7c03d63168fccee5038a62f469469ed6a4dd6eaeb9338abedcd0d5f5 \
-    --hash=sha256:f450fcbae214aae66bd9d2b9af48e0f8ba1cb0e8596c6ebb34e6e3f0fec6542c \
-    --hash=sha256:f870d14a587ea58a3b596aa994c2ed889cc051f9e450e887d2c83656fc6a64bf
+statsmodels==0.14.5 ; python_version >= "3.11" \
+    --hash=sha256:128872be8f3208f4446d91ea9e4261823902fc7997fee7e1a983eb62fd3b7c6e \
+    --hash=sha256:145bc39b2cb201efb6c83cc3f2163c269e63b0d4809801853dec6f440bd3bc37 \
+    --hash=sha256:1cab9e6fce97caf4239cdb2df375806937da5d0b7ba2699b13af33a07f438464 \
+    --hash=sha256:1e9742d8a5ac38a3bfc4b7f4b0681903920f20cbbf466d72b1fd642033846108 \
+    --hash=sha256:26c028832730aebfbfd4e7501694e1f9ad31ec8536e776716673f4e7afd4059a \
+    --hash=sha256:2a06bca03b7a492f88c8106103ab75f1a5ced25de90103a89f3a287518017939 \
+    --hash=sha256:37e7364a39f9aa3b51d15a208c2868b90aadb8412f868530f5cba9197cb00eaa \
+    --hash=sha256:4263d7f4d0f1d5ac6eb4db22e1ee34264a14d634b9332c975c9d9109b6b46e12 \
+    --hash=sha256:4a060c7e0841c549c8ce2825fd6687e6757e305d9c11c9a73f6c5a0ce849bb69 \
+    --hash=sha256:4b7091a8442076c708c926de3603653a160955e80a2b6d931475b7bb8ddc02e5 \
+    --hash=sha256:4e5e26b21d2920905764fb0860957d08b5ba2fae4466ef41b1f7c53ecf9fc7fa \
+    --hash=sha256:56da20def5350d676388213a330fd40ed15d0e8dd0bb1b92c0e4b0f2a65d3ad2 \
+    --hash=sha256:5a085d47c8ef5387279a991633883d0e700de2b0acc812d7032d165888627bef \
+    --hash=sha256:6264fb00e02f858b86bd01ef2dc05055a71d4a0cc7551b9976b07b0f0e6cf24f \
+    --hash=sha256:86224f6e36f38486e471e75759d241fe2912d8bc25ab157d54ee074c6aedbf45 \
+    --hash=sha256:906263134dd1a640e55ecb01fda4a9be7b9e08558dba9e4c4943a486fdb0c9c8 \
+    --hash=sha256:9118f76344f77cffbb3a9cbcff8682b325be5eed54a4b3253e09da77a74263d3 \
+    --hash=sha256:9dc4ee159070557c9a6c000625d85f653de437772fe7086857cff68f501afe45 \
+    --hash=sha256:9f866b2ebb2904b47c342d00def83c526ef2eb1df6a9a3c94ba5fe63d0005aec \
+    --hash=sha256:9fc2b5cdc0c95cba894849651fec1fa1511d365e3eb72b0cc75caac44077cd48 \
+    --hash=sha256:afb37ca1d70d99b5fd876e8574ea46372298ae0f0a8b17e4cf0a9afd2373ae62 \
+    --hash=sha256:b23b8f646dd78ef5e8d775d879208f8dc0a73418b41c16acac37361ff9ab7738 \
+    --hash=sha256:b2ed065bfbaf8bb214c7201656df840457c2c8c65e1689e3eb09dc7440f9c61c \
+    --hash=sha256:b8d96b0bbaeabd3a557c35cc7249baa9cfbc6dd305c32a9f2cbdd7f46c037e7f \
+    --hash=sha256:c3dd760a6fa80cd5e0371685c697bb9c2c0e6e1f394d975e596a1e6d0bbb9372 \
+    --hash=sha256:d7c14fb2617bb819fb2532e1424e1da2b98a3419a80e95f33365a72d437d474e \
+    --hash=sha256:de260e58cccfd2ceddf835b55a357233d6ca853a1aa4f90f7553a52cc71c6ddf \
+    --hash=sha256:ec56f771d9529cdc17ed2fb2a950d100b6e83a7c5372aae8ac5bb065c474b856 \
+    --hash=sha256:f2ad5aee04ae7196c429df2174df232c057e478c5fa63193d01c8ec9aae04d31 \
+    --hash=sha256:f402fc793458dd6d96e099acb44cd1de1428565bf7ef3030878a8daff091f08a
 texttable==1.7.0 ; python_version >= "3.11" \
     --hash=sha256:2d2068fb55115807d3ac77a4ca68fa48803e84ebb0ee2340f858107a36522638 \
     --hash=sha256:72227d592c82b3d7f672731ae73e4d1f88cd8e2ef5b075a7a7f01a23a3743917
@@ -908,6 +967,9 @@ typing-extensions==4.15.0 ; python_version >= "3.11" \
 tzdata==2024.1 ; python_version >= "3.11" \
     --hash=sha256:2674120f8d891909751c38abcdfd386ac0a5a1127954fbc332af6b5ceae07efd \
     --hash=sha256:9068bc196136463f5245e51efda838afa15aaeca9903f49050dfa2679db4d252
+umap-learn==0.5.7 ; python_version >= "3.11" \
+    --hash=sha256:6a7e0be2facfa365a5ed6588447102bdbef32a0ef449535c25c97ea7e680073c \
+    --hash=sha256:b2a97973e4c6ffcebf241100a8de589a4c84126a832ab40f296c6d9fcc5eb19e
 urllib3==2.4.0 ; python_version >= "3.11" \
     --hash=sha256:414bc6535b787febd7567804cc015fee39daab8ad86268f1310a9250697de466 \
     --hash=sha256:4e16665048960a0900c702d4a66415956a584919c03361cac9f1df5c5dd7e813