spacr 0.3.47__py3-none-any.whl → 0.3.52__py3-none-any.whl

spacr/utils.py

@@ -4067,7 +4067,7 @@ def generate_path_list_from_db(db_path, file_metadata):
     
     return all_paths
 
-def correct_paths(df, base_path):
+def correct_paths(df, base_path, folder='data'):
 
     if isinstance(df, pd.DataFrame):
 
@@ -4083,9 +4083,9 @@ def correct_paths(df, base_path):
     adjusted_image_paths = []
     for path in image_paths:
         if base_path not in path:
-            parts = path.split('/data/')
+            parts = path.split(f'/{folder}/')
             if len(parts) > 1:
-                new_path = os.path.join(base_path, 'data', parts[1])
+                new_path = os.path.join(base_path, f'{folder}', parts[1])
                 adjusted_image_paths.append(new_path)
             else:
                 adjusted_image_paths.append(path)
@@ -5224,4 +5224,35 @@ def correct_metadata_column_names(df):
         df = df.rename(columns={'grna_name': 'grna'})
     if 'plate_row' in df.columns:
         df[['plate', 'row']] = df['plate_row'].str.split('_', expand=True)
-    return df
+    return df
+
+def control_filelist(folder, mode='column', values=['01','02']):
+    files = os.listdir(folder)
+    if mode is 'column':
+        filtered_files = [file for file in files if file.split('_')[1][1:] in values]
+    if mode is 'row':
+        filtered_files = [file for file in files if file.split('_')[1][:1] in values]
+    return filtered_files
+
+def choose_p_adjust_method(num_groups, num_data_points):
+    """
+    Selects the most appropriate p-value adjustment method based on data characteristics.
+    
+    Parameters:
+    - num_groups: Number of unique groups being compared
+    - num_data_points: Number of data points per group (assuming balanced groups)
+    
+    Returns:
+    - A string representing the recommended p-adjustment method
+    """
+    num_comparisons = (num_groups * (num_groups - 1)) // 2  # Number of pairwise comparisons
+
+    # Decision logic for choosing the adjustment method
+    if num_comparisons <= 10 and num_data_points > 5:
+        return 'holm'  # Balanced between power and Type I error control
+    elif num_comparisons > 10 and num_data_points <= 5:
+        return 'fdr_bh'  # FDR control for large number of comparisons and small sample size
+    elif num_comparisons <= 10:
+        return 'sidak'  # Less conservative than Bonferroni, good for independent comparisons
+    else:
+        return 'bonferroni'  # Very conservative, use for strict control of Type I errors

{spacr-0.3.47.dist-info → spacr-0.3.52.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spacr
-Version: 0.3.47
+Version: 0.3.52
 Summary: Spatial phenotype analysis of crisp screens (SpaCr)
 Home-page: https://github.com/EinarOlafsson/spacr
 Author: Einar Birnir Olafsson
@@ -16,6 +16,7 @@ Requires-Dist: scipy<2.0,>=1.12.0
 Requires-Dist: cellpose<4.0,>=3.0.6
 Requires-Dist: scikit-image<1.0,>=0.22.0
 Requires-Dist: scikit-learn<2.0,>=1.4.1
+Requires-Dist: scikit-posthocs<0.20,>=0.10.0
 Requires-Dist: mahotas<2.0,>=1.4.13
 Requires-Dist: btrack<1.0,>=0.6.5
 Requires-Dist: trackpy<1.0,>=0.6.2
@@ -66,6 +67,7 @@ Requires-Dist: gdown
 Requires-Dist: IPython<9.0,>=8.18.1
 Requires-Dist: ipykernel
 Requires-Dist: ipywidgets<9.0,>=8.1.2
+Requires-Dist: brokenaxes<1.0,>=0.6.2
 Requires-Dist: huggingface-hub<0.25,>=0.24.0
 Provides-Extra: dev
 Requires-Dist: pytest<3.11,>=3.9; extra == "dev"

{spacr-0.3.47.dist-info → spacr-0.3.52.dist-info}/RECORD

@@ -8,26 +8,27 @@ spacr/app_measure.py,sha256=_K7APYIeOKpV6e_LcqabBjvEi7mfq9Fch8175x1x0k8,162
 spacr/app_sequencing.py,sha256=DjG26jy4cpddnV8WOOAIiExtOe9MleVMY4MFa5uTo5w,157
 spacr/app_umap.py,sha256=ZWAmf_OsIKbYvolYuWPMYhdlVe-n2CADoJulAizMiEo,153
 spacr/cellpose.py,sha256=RBHMs2vwXcfkj0xqAULpALyzJYXddSRycgZSzmwI7v0,14755
+spacr/chat_bot.py,sha256=n3Fhqg3qofVXHmh3H9sUcmfYy9MmgRnr48663MVdY9E,1244
 spacr/core.py,sha256=dW9RrAKFLfVsFhX0-kaVMc2T7b47Ky0pTXK-CEVOeWQ,48235
 spacr/deep_spacr.py,sha256=HdOcNU8cHcE_19nP7_5uTz-ih3E169ffr2Hm--NvMvA,43255
 spacr/gui.py,sha256=ARyn9Q_g8HoP-cXh1nzMLVFCKqthY4v2u9yORyaQqQE,8230
 spacr/gui_core.py,sha256=N7R7yvfK_dJhOReM_kW3Ci8Bokhi1OzsxeKqvSGdvV4,41460
-spacr/gui_elements.py,sha256=w-S1MZdyxt5O3DsNAHNNXy_WGfwBPg0NhwQtCsJeiao,137071
-spacr/gui_utils.py,sha256=KDWDWsi7UdZVhXk1ZWGx3ZqJMIxCUm3lGfjrVhbk52s,45463
+spacr/gui_elements.py,sha256=Dr9KEek41LggJ2z2zfh28a7w86sZXg1jzF388rF2BT4,138249
+spacr/gui_utils.py,sha256=aOVI2G71pObolEjuSgAKr86XJZtN98uqqBfCbucMhRQ,45560
 spacr/io.py,sha256=1rIdJ_8dyn7W4D2zXjaOqlgyo_Y5Z7X86aRp4hNYWCU,144194
 spacr/logger.py,sha256=lJhTqt-_wfAunCPl93xE65Wr9Y1oIHJWaZMjunHUeIw,1538
-spacr/measure.py,sha256=KdboGXoi85BO5-_6er7932FgjFI7G7tuaQDnWSiEuew,54817
+spacr/measure.py,sha256=euywVbBXRllht-frnxy9QHV76i8HkPPjm3dJw46kcz0,55085
 spacr/mediar.py,sha256=FwLvbLQW5LQzPgvJZG8Lw7GniA2vbZx6Jv6vIKu7I5c,14743
-spacr/ml.py,sha256=Mkxl4n3OvNsVix8bbPQ09-HTgP3YTzQOESso4_exKLs,54634
+spacr/ml.py,sha256=Oykp3drBxZrcwrWQh2n6Xt1OzZER6pSIiaR-W0GO2_E,67353
 spacr/openai.py,sha256=5vBZ3Jl2llYcW3oaTEXgdyCB2aJujMUIO5K038z7w_A,1246
-spacr/plot.py,sha256=M04Cbv1n_FHxO0Qg3VNu_IQXRGt7lb-sgWzh9jjL4rI,145733
-spacr/sequencing.py,sha256=aP2QUfb9wpeJRZFLWFwxq1o4EtVpSvyVohOcm3Wvrq0,24965
-spacr/settings.py,sha256=XEpo9sQXmQ3-sdRNmcsss6q0j7ZAvoAFO-_D8ecgYQc,77710
+spacr/plot.py,sha256=B4nxp7NFyM6MmtarW9zbxydeEvVIMgPqHEElkCIycpA,169566
+spacr/sequencing.py,sha256=HDpF_C3hRd-fk6ZENPmI3vgYoom3HIvaeIIZWLhaIAY,25037
+spacr/settings.py,sha256=2Er3G6ApcemIEhyQCsF8zmVdBW8KiKf4nkSismu03s8,77358
 spacr/sim.py,sha256=1xKhXimNU3ukzIw-3l9cF3Znc_brW8h20yv8fSTzvss,71173
 spacr/submodules.py,sha256=3C5M4UbI9Ral1MX4PTpucaAaqhL3RADuCOCqaHhMyUg,28048
 spacr/timelapse.py,sha256=FSYpUtAVy6xc3lwprRYgyDTT9ysUhfRQ4zrP9_h2mvg,39465
-spacr/toxo.py,sha256=RjAqI2sCcYYr-eiLPGnyJUn96zR_ATENuyiM2CZT408,13358
-spacr/utils.py,sha256=zkgUP_w_w9HJe4000KhVmpwO2gELoeIvdYNrXlRAzG8,221050
+spacr/toxo.py,sha256=bcH5Ug6xtf3BBxvOFc8e4Jc5R3f6-C46oHhgiSoYl3U,24935
+spacr/utils.py,sha256=clrjlUOhY-LQH0bTIiNJ9VMBEU9qlRbTvoU7-yNLzsg,222475
 spacr/version.py,sha256=axH5tnGwtgSnJHb5IDhiu4Zjk5GhLyAEDRe-rnaoFOA,409
 spacr/resources/MEDIAR/.gitignore,sha256=Ff1q9Nme14JUd-4Q3jZ65aeQ5X4uttptssVDgBVHYo8,152
 spacr/resources/MEDIAR/LICENSE,sha256=yEj_TRDLUfDpHDNM0StALXIt6mLqSgaV2hcCwa6_TcY,1065
@@ -150,9 +151,9 @@ spacr/resources/icons/umap.png,sha256=dOLF3DeLYy9k0nkUybiZMe1wzHQwLJFRmgccppw-8b
 spacr/resources/images/plate1_E01_T0001F001L01A01Z01C02.tif,sha256=Tl0ZUfZ_AYAbu0up_nO0tPRtF1BxXhWQ3T3pURBCCRo,7958528
 spacr/resources/images/plate1_E01_T0001F001L01A02Z01C01.tif,sha256=m8N-V71rA1TT4dFlENNg8s0Q0YEXXs8slIn7yObmZJQ,7958528
 spacr/resources/images/plate1_E01_T0001F001L01A03Z01C03.tif,sha256=Pbhk7xn-KUP6RSIhJsxQcrHFImBm3GEpLkzx7WOc-5M,7958528
-spacr-0.3.47.dist-info/LICENSE,sha256=SR-2MeGc6SCM1UORJYyarSWY_A-JaOMFDj7ReSs9tRM,1083
-spacr-0.3.47.dist-info/METADATA,sha256=NEQNKKM40sYjqLkD1M-R4eOVTPSAQJ4zDD_5juTElbk,5949
-spacr-0.3.47.dist-info/WHEEL,sha256=HiCZjzuy6Dw0hdX5R3LCFPDmFS4BWl8H-8W39XfmgX4,91
-spacr-0.3.47.dist-info/entry_points.txt,sha256=BMC0ql9aNNpv8lUZ8sgDLQMsqaVnX5L535gEhKUP5ho,296
-spacr-0.3.47.dist-info/top_level.txt,sha256=GJPU8FgwRXGzKeut6JopsSRY2R8T3i9lDgya42tLInY,6
-spacr-0.3.47.dist-info/RECORD,,
+spacr-0.3.52.dist-info/LICENSE,sha256=SR-2MeGc6SCM1UORJYyarSWY_A-JaOMFDj7ReSs9tRM,1083
+spacr-0.3.52.dist-info/METADATA,sha256=I0OCX9zCPvfgnnGS2JYaV-vdNvirglSfO6IzX68s8uI,6032
+spacr-0.3.52.dist-info/WHEEL,sha256=HiCZjzuy6Dw0hdX5R3LCFPDmFS4BWl8H-8W39XfmgX4,91
+spacr-0.3.52.dist-info/entry_points.txt,sha256=BMC0ql9aNNpv8lUZ8sgDLQMsqaVnX5L535gEhKUP5ho,296
+spacr-0.3.52.dist-info/top_level.txt,sha256=GJPU8FgwRXGzKeut6JopsSRY2R8T3i9lDgya42tLInY,6
+spacr-0.3.52.dist-info/RECORD,,