cfi-toolkit 0.1.0__tar.gz → 0.1.1__tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (7) hide show
  1. {cfi_toolkit-0.1.0 → cfi_toolkit-0.1.1}/PKG-INFO +24 -24
  2. {cfi_toolkit-0.1.0 → cfi_toolkit-0.1.1}/README.md +23 -23
  3. {cfi_toolkit-0.1.0 → cfi_toolkit-0.1.1}/cfi_toolkit/__init__.py +1 -1
  4. {cfi_toolkit-0.1.0 → cfi_toolkit-0.1.1}/pyproject.toml +1 -1
  5. {cfi_toolkit-0.1.0 → cfi_toolkit-0.1.1}/LICENSE +0 -0
  6. {cfi_toolkit-0.1.0 → cfi_toolkit-0.1.1}/cfi_toolkit/CellFunctionality.py +0 -0
  7. {cfi_toolkit-0.1.0 → cfi_toolkit-0.1.1}/cfi_toolkit/CellGraph.py +0 -0
{cfi_toolkit-0.1.0 → cfi_toolkit-0.1.1}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: cfi-toolkit
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- Version: 0.1.0
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+ Version: 0.1.1
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  Summary: CFI: Cell Functionality and Interaction Analysis Tool
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  License: GPL-3
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  License-File: LICENSE
@@ -56,7 +56,7 @@ CFI extends these capabilities by enabling the identification of direct cell–c
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  <p align="center">
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- <img src="fig/log.png" alt="drawing" width="500" />
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+ <img src="https://github.com/jkubis96/CFI/raw/refs/heads/lib_merging/fig/log.png" alt="drawing" width="500" />
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  </p>
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@@ -111,7 +111,7 @@ In the case of interactions network analyses, it is recommended to use the [JVe
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  #### In command line write:
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  ```
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- pip install cfi
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+ pip install cfi-toolkit
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  ```
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@@ -139,7 +139,7 @@ Documentation for classes and functions is available here 👉 [Documentation
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  import os
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  from jdti import COMPsc # JDtI module for handling single-cell projects
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- from cfi import CellFunCon # Cell functional connectivity / enrichment analysis
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+ from cfi_toolkit import CellFunCon # Cell functional connectivity / enrichment analysis
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  # ------------------------------------------------------------
@@ -251,7 +251,7 @@ data = instance.get_enrichment_data(
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  Visualization
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  ```
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- from cfi import encrichment_cell_heatmap
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+ from cfi_toolkit import encrichment_cell_heatmap
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  fig = encrichment_cell_heatmap(data = data,
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  fig_size = (3,3),
@@ -267,7 +267,7 @@ fig = encrichment_cell_heatmap(data = data,
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  <p align="center">
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- <img src="fig/heatmap.svg" alt="drawing" width="450" />
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+ <img src="https://github.com/jkubis96/CFI/raw/refs/heads/lib_merging/fig/heatmap.svg" alt="drawing" width="450" />
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  </p>
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273
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@@ -297,7 +297,7 @@ data = instance.get_enrichment_data(
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  Visualization
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299
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  ```
300
- from cfi import encrichment_cell_heatmap
300
+ from cfi_toolkit import encrichment_cell_heatmap
301
301
 
302
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  fig = encrichment_cell_heatmap(data = enr,
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  fig_size = (3,3),
@@ -313,7 +313,7 @@ fig = encrichment_cell_heatmap(data = enr,
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313
 
314
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  <p align="center">
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- <img src="fig/heatmap2.svg" alt="drawing" width="450" />
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+ <img src="https://github.com/jkubis96/CFI/raw/refs/heads/lib_merging/fig/heatmap2.svg" alt="drawing" width="450" />
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  </p>
318
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319
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@@ -327,7 +327,7 @@ fig = encrichment_cell_heatmap(data = enr,
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  Visualization
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329
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  ```
330
- from cfi import encrichment_cell_heatmap
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+ from cfi_toolkit import encrichment_cell_heatmap
331
331
 
332
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  fig2 = encrichment_cell_heatmap(data = enr,
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  fig_size = (3,3),
@@ -348,7 +348,7 @@ fig2 = encrichment_cell_heatmap(data = enr,
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  <p align="center">
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- <img src="fig/heatmap3.svg" alt="drawing" width="450" />
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+ <img src="https://github.com/jkubis96/CFI/raw/refs/heads/lib_merging/fig/heatmap3.svg" alt="drawing" width="450" />
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  </p>
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@@ -380,7 +380,7 @@ data = instance.get_enrichment_data(
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  Visualization
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382
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  ```
383
- from cfi import encrichment_cell_heatmap
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+ from cfi_toolkit import encrichment_cell_heatmap
384
384
 
385
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  fig = encrichment_cell_heatmap(data = enr,
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  fig_size = (3,3),
@@ -396,7 +396,7 @@ fig = encrichment_cell_heatmap(data = enr,
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398
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  <p align="center">
399
- <img src="fig/heatmap4.svg" alt="drawing" width="450" />
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+ <img src="https://github.com/jkubis96/CFI/raw/refs/heads/lib_merging/fig/heatmap4.svg" alt="drawing" width="450" />
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  </p>
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@@ -427,7 +427,7 @@ data = instance.get_enrichment_data(
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  Visualization
428
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429
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  ```
430
- from cfi import encrichment_cell_heatmap
430
+ from cfi_toolkit import encrichment_cell_heatmap
431
431
 
432
432
  fig = encrichment_cell_heatmap(data = enr,
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  fig_size = (3,3),
@@ -443,7 +443,7 @@ fig = encrichment_cell_heatmap(data = enr,
443
443
 
444
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445
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  <p align="center">
446
- <img src="fig/heatmap5.svg" alt="drawing" width="450" />
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+ <img src="https://github.com/jkubis96/CFI/raw/refs/heads/lib_merging/fig/heatmap5.svg" alt="drawing" width="450" />
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  </p>
448
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449
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  <br />
@@ -463,7 +463,7 @@ instance.get_included_cells()
463
463
  ```
464
464
 
465
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  <p align="center">
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- <img src="fig/out_cell.bmp" alt="drawing" width="450" />
466
+ <img src="https://github.com/jkubis96/CFI/raw/refs/heads/lib_merging/fig/out_cell.bmp" alt="drawing" width="450" />
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467
  </p>
468
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469
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@@ -489,7 +489,7 @@ cell_int = instance.get_gene_interactions('STRIATUM_1 # s1')
489
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  Visualization
490
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491
491
  ```
492
- from cfi import gene_interaction_network
492
+ from cfi_toolkit import gene_interaction_network
493
493
 
494
494
  fig5 = gene_interaction_network(idata = cell_int, min_con = 2)
495
495
 
@@ -501,7 +501,7 @@ nt.edit()
501
501
 
502
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503
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  <p align="center">
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- <img src="fig/gin.bmp" alt="drawing" width="300" />
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+ <img src="https://github.com/jkubis96/CFI/raw/refs/heads/lib_merging/fig/gin.bmp" alt="drawing" width="300" />
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505
  </p>
506
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507
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  <br />
@@ -545,7 +545,7 @@ cell_con = instance.get_cell_connections()
545
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  Visualization
546
546
 
547
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  ```
548
- from cfi import draw_cell_conections
548
+ from cfi_toolkit import draw_cell_conections
549
549
 
550
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  fig = draw_cell_conections(cell_con)
551
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@@ -556,7 +556,7 @@ nt.edit()
556
556
  ```
557
557
 
558
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  <p align="center">
559
- <img src="fig/cell_con.bmp" alt="drawing" width="300" />
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+ <img src="https://github.com/jkubis96/CFI/raw/refs/heads/lib_merging/fig/cell_con.bmp" alt="drawing" width="300" />
560
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  </p>
561
561
 
562
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  <br />
@@ -576,7 +576,7 @@ instance.save_project('project')
576
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  Loading previously saved project
577
577
 
578
578
  ```
579
- from cfi import CellFunCon
579
+ from cfi_toolkit import CellFunCon
580
580
 
581
581
  instance = CellFunCon.load_project('project.psc')
582
582
  ```
@@ -595,7 +595,7 @@ instance = CellFunCon.load_project('project.psc')
595
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  # ------------------------------------------------------------
596
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  import os
597
597
  from jdti import COMPsc # JDtI module for single-cell project handling
598
- from cfi import CellFunCon # Functional analysis and cell interaction inference
598
+ from cfi_toolkit import CellFunCon # Functional analysis and cell interaction inference
599
599
 
600
600
 
601
601
  # ------------------------------------------------------------
@@ -666,7 +666,7 @@ instance2.calculate_cell_connections()
666
666
  # - healthy condition
667
667
  # - disease condition
668
668
 
669
- from cfi import compare_connections
669
+ from cfi_toolkit import compare_connections
670
670
 
671
671
  instances_dict = {
672
672
  "healthy": instance2,
@@ -697,7 +697,7 @@ comparison = compare_connections(instances_dict=instances_dict,
697
697
  Visualization
698
698
 
699
699
  ```
700
- from cfi import volcano_plot_conections
700
+ from cfi_toolkit import volcano_plot_conections
701
701
 
702
702
  fig = volcano_plot_conections(
703
703
  deg_data = comparison,
@@ -714,7 +714,7 @@ fig = volcano_plot_conections(
714
714
 
715
715
 
716
716
  <p align="center">
717
- <img src="fig/volcano.svg" alt="drawing" width="450" />
717
+ <img src="https://github.com/jkubis96/CFI/raw/refs/heads/lib_merging/fig/volcano.svg" alt="drawing" width="450" />
718
718
  </p>
719
719
 
720
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{cfi_toolkit-0.1.0 → cfi_toolkit-0.1.1}/README.md RENAMED
@@ -34,7 +34,7 @@ CFI extends these capabilities by enabling the identification of direct cell–c
34
34
 
35
35
 
36
36
  <p align="center">
37
- <img src="fig/log.png" alt="drawing" width="500" />
37
+ <img src="https://github.com/jkubis96/CFI/raw/refs/heads/lib_merging/fig/log.png" alt="drawing" width="500" />
38
38
  </p>
39
39
 
40
40
 
@@ -89,7 +89,7 @@ In the case of interactions network analyses, it is recommended to use the [JVe
89
89
  #### In command line write:
90
90
 
91
91
  ```
92
- pip install cfi
92
+ pip install cfi-toolkit
93
93
  ```
94
94
 
95
95
 
@@ -117,7 +117,7 @@ Documentation for classes and functions is available here 👉 [Documentation
117
117
 
118
118
  import os
119
119
  from jdti import COMPsc # JDtI module for handling single-cell projects
120
- from cfi import CellFunCon # Cell functional connectivity / enrichment analysis
120
+ from cfi_toolkit import CellFunCon # Cell functional connectivity / enrichment analysis
121
121
 
122
122
 
123
123
  # ------------------------------------------------------------
@@ -229,7 +229,7 @@ data = instance.get_enrichment_data(
229
229
  Visualization
230
230
 
231
231
  ```
232
- from cfi import encrichment_cell_heatmap
232
+ from cfi_toolkit import encrichment_cell_heatmap
233
233
 
234
234
  fig = encrichment_cell_heatmap(data = data,
235
235
  fig_size = (3,3),
@@ -245,7 +245,7 @@ fig = encrichment_cell_heatmap(data = data,
245
245
 
246
246
 
247
247
  <p align="center">
248
- <img src="fig/heatmap.svg" alt="drawing" width="450" />
248
+ <img src="https://github.com/jkubis96/CFI/raw/refs/heads/lib_merging/fig/heatmap.svg" alt="drawing" width="450" />
249
249
  </p>
250
250
 
251
251
 
@@ -275,7 +275,7 @@ data = instance.get_enrichment_data(
275
275
  Visualization
276
276
 
277
277
  ```
278
- from cfi import encrichment_cell_heatmap
278
+ from cfi_toolkit import encrichment_cell_heatmap
279
279
 
280
280
  fig = encrichment_cell_heatmap(data = enr,
281
281
  fig_size = (3,3),
@@ -291,7 +291,7 @@ fig = encrichment_cell_heatmap(data = enr,
291
291
 
292
292
 
293
293
  <p align="center">
294
- <img src="fig/heatmap2.svg" alt="drawing" width="450" />
294
+ <img src="https://github.com/jkubis96/CFI/raw/refs/heads/lib_merging/fig/heatmap2.svg" alt="drawing" width="450" />
295
295
  </p>
296
296
 
297
297
 
@@ -305,7 +305,7 @@ fig = encrichment_cell_heatmap(data = enr,
305
305
  Visualization
306
306
 
307
307
  ```
308
- from cfi import encrichment_cell_heatmap
308
+ from cfi_toolkit import encrichment_cell_heatmap
309
309
 
310
310
  fig2 = encrichment_cell_heatmap(data = enr,
311
311
  fig_size = (3,3),
@@ -326,7 +326,7 @@ fig2 = encrichment_cell_heatmap(data = enr,
326
326
 
327
327
 
328
328
  <p align="center">
329
- <img src="fig/heatmap3.svg" alt="drawing" width="450" />
329
+ <img src="https://github.com/jkubis96/CFI/raw/refs/heads/lib_merging/fig/heatmap3.svg" alt="drawing" width="450" />
330
330
  </p>
331
331
 
332
332
 
@@ -358,7 +358,7 @@ data = instance.get_enrichment_data(
358
358
  Visualization
359
359
 
360
360
  ```
361
- from cfi import encrichment_cell_heatmap
361
+ from cfi_toolkit import encrichment_cell_heatmap
362
362
 
363
363
  fig = encrichment_cell_heatmap(data = enr,
364
364
  fig_size = (3,3),
@@ -374,7 +374,7 @@ fig = encrichment_cell_heatmap(data = enr,
374
374
 
375
375
 
376
376
  <p align="center">
377
- <img src="fig/heatmap4.svg" alt="drawing" width="450" />
377
+ <img src="https://github.com/jkubis96/CFI/raw/refs/heads/lib_merging/fig/heatmap4.svg" alt="drawing" width="450" />
378
378
  </p>
379
379
 
380
380
 
@@ -405,7 +405,7 @@ data = instance.get_enrichment_data(
405
405
  Visualization
406
406
 
407
407
  ```
408
- from cfi import encrichment_cell_heatmap
408
+ from cfi_toolkit import encrichment_cell_heatmap
409
409
 
410
410
  fig = encrichment_cell_heatmap(data = enr,
411
411
  fig_size = (3,3),
@@ -421,7 +421,7 @@ fig = encrichment_cell_heatmap(data = enr,
421
421
 
422
422
 
423
423
  <p align="center">
424
- <img src="fig/heatmap5.svg" alt="drawing" width="450" />
424
+ <img src="https://github.com/jkubis96/CFI/raw/refs/heads/lib_merging/fig/heatmap5.svg" alt="drawing" width="450" />
425
425
  </p>
426
426
 
427
427
  <br />
@@ -441,7 +441,7 @@ instance.get_included_cells()
441
441
  ```
442
442
 
443
443
  <p align="center">
444
- <img src="fig/out_cell.bmp" alt="drawing" width="450" />
444
+ <img src="https://github.com/jkubis96/CFI/raw/refs/heads/lib_merging/fig/out_cell.bmp" alt="drawing" width="450" />
445
445
  </p>
446
446
 
447
447
 
@@ -467,7 +467,7 @@ cell_int = instance.get_gene_interactions('STRIATUM_1 # s1')
467
467
  Visualization
468
468
 
469
469
  ```
470
- from cfi import gene_interaction_network
470
+ from cfi_toolkit import gene_interaction_network
471
471
 
472
472
  fig5 = gene_interaction_network(idata = cell_int, min_con = 2)
473
473
 
@@ -479,7 +479,7 @@ nt.edit()
479
479
 
480
480
 
481
481
  <p align="center">
482
- <img src="fig/gin.bmp" alt="drawing" width="300" />
482
+ <img src="https://github.com/jkubis96/CFI/raw/refs/heads/lib_merging/fig/gin.bmp" alt="drawing" width="300" />
483
483
  </p>
484
484
 
485
485
  <br />
@@ -523,7 +523,7 @@ cell_con = instance.get_cell_connections()
523
523
  Visualization
524
524
 
525
525
  ```
526
- from cfi import draw_cell_conections
526
+ from cfi_toolkit import draw_cell_conections
527
527
 
528
528
  fig = draw_cell_conections(cell_con)
529
529
 
@@ -534,7 +534,7 @@ nt.edit()
534
534
  ```
535
535
 
536
536
  <p align="center">
537
- <img src="fig/cell_con.bmp" alt="drawing" width="300" />
537
+ <img src="https://github.com/jkubis96/CFI/raw/refs/heads/lib_merging/fig/cell_con.bmp" alt="drawing" width="300" />
538
538
  </p>
539
539
 
540
540
  <br />
@@ -554,7 +554,7 @@ instance.save_project('project')
554
554
  Loading previously saved project
555
555
 
556
556
  ```
557
- from cfi import CellFunCon
557
+ from cfi_toolkit import CellFunCon
558
558
 
559
559
  instance = CellFunCon.load_project('project.psc')
560
560
  ```
@@ -573,7 +573,7 @@ instance = CellFunCon.load_project('project.psc')
573
573
  # ------------------------------------------------------------
574
574
  import os
575
575
  from jdti import COMPsc # JDtI module for single-cell project handling
576
- from cfi import CellFunCon # Functional analysis and cell interaction inference
576
+ from cfi_toolkit import CellFunCon # Functional analysis and cell interaction inference
577
577
 
578
578
 
579
579
  # ------------------------------------------------------------
@@ -644,7 +644,7 @@ instance2.calculate_cell_connections()
644
644
  # - healthy condition
645
645
  # - disease condition
646
646
 
647
- from cfi import compare_connections
647
+ from cfi_toolkit import compare_connections
648
648
 
649
649
  instances_dict = {
650
650
  "healthy": instance2,
@@ -675,7 +675,7 @@ comparison = compare_connections(instances_dict=instances_dict,
675
675
  Visualization
676
676
 
677
677
  ```
678
- from cfi import volcano_plot_conections
678
+ from cfi_toolkit import volcano_plot_conections
679
679
 
680
680
  fig = volcano_plot_conections(
681
681
  deg_data = comparison,
@@ -692,7 +692,7 @@ fig = volcano_plot_conections(
692
692
 
693
693
 
694
694
  <p align="center">
695
- <img src="fig/volcano.svg" alt="drawing" width="450" />
695
+ <img src="https://github.com/jkubis96/CFI/raw/refs/heads/lib_merging/fig/volcano.svg" alt="drawing" width="450" />
696
696
  </p>
697
697
 
698
698
 
{cfi_toolkit-0.1.0 → cfi_toolkit-0.1.1}/cfi_toolkit/__init__.py RENAMED
@@ -18,5 +18,5 @@ from .CellFunctionality import *
18
18
  from .CellGraph import *
19
19
 
20
20
  print("")
21
- print("Welcome in CFI v.0.0.1 library")
21
+ print("Welcome in CFI v.0.1.1 library")
22
22
  print("")
{cfi_toolkit-0.1.0 → cfi_toolkit-0.1.1}/pyproject.toml RENAMED
@@ -1,6 +1,6 @@
1
1
  [project]
2
2
  name = "cfi-toolkit"
3
- version = "0.1.0"
3
+ version = "0.1.1"
4
4
  description = "CFI: Cell Functionality and Interaction Analysis Tool"
5
5
  readme = "README.md"
6
6
 
{cfi_toolkit-0.1.0 → cfi_toolkit-0.1.1}/LICENSE RENAMED
File without changes