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Edit 4_processing_features module #17

Merged
merged 7 commits into from
Nov 28, 2022
Merged

Edit 4_processing_features module #17

merged 7 commits into from
Nov 28, 2022

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jenna-tomkinson
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@gwaybio

Here is the PR for the preprocessing features module with all the edits and the README included.

@jenna-tomkinson jenna-tomkinson changed the title edit data and create readme Edit 4_preprocessing_features module Nov 14, 2022
@jenna-tomkinson jenna-tomkinson changed the title Edit 4_preprocessing_features module Edit 4_processing_features module Nov 14, 2022
@gwaybio gwaybio self-requested a review November 15, 2022 01:17
@gwaybio gwaybio mentioned this pull request Nov 15, 2022
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gwaybio
gwaybio approved these changes Nov 15, 2022
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Looks great 🤩

I made one suggestion, asked a question, and opened #18 in case we need to change other modules.

Depending on your answer to my question, I may need to take another look at this PR.

4_processing_features/README.md Outdated Show resolved Hide resolved
4_processing_features/README.md

---

## Step 1: Setup Processing Feature Environment
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I suppose that we'll add the next steps in a future PR?

Although maybe it belongs here? What else would belong in this module?

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@gwaybio

I guess what do you mean by next steps? I just added what I understood was going on.

Would we want to add steps for performing statistics or do you mean something else?

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Wouldn't next steps be instructions on how to run the preprocessing notebook?

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Oh... you are right lol

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My bad, brain was not thinking about that! I will add that and make the commit when I am back! 😄

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@gwaybio

Just added the instructions and file to run the notebook. Please review when you have a chance! 😄

gwaybio
gwaybio approved these changes Nov 28, 2022
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LGTM

4_processing_features/README.md

## Step 2: Normalize Single Cell Features

### Step 2a: Set Up Paths
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I don't think this step is necessary. This notebook contains only relative paths that should work generically on any machine, right?

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Well they might put the output from CellProfiler in a different folder. The step is more of an as needed type of deal. I don't think that my pipeline specifically puts the sqlite file in the Analysis_Output folder (I think I did this manually).

I think it is good to leave in their in case the user changes things and doesn't understand why it is not working.

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@gwaybio Merging now!

@jenna-tomkinson jenna-tomkinson merged commit 1e70c20 into WayScience:main Nov 28, 2022
@jenna-tomkinson jenna-tomkinson deleted the edit_features_module branch November 28, 2022 20:10
d33bs added a commit to d33bs/NF1_SchwannCell_data that referenced this pull request Jan 31, 2023
@d33bs
Squashed commit of the following:
9405ef7 
commit fc76764
Merge: 0ba2392 d2b68b7
Author: Jenna Tomkinson <107513215+jenna-tomkinson@users.noreply.github.com>
Date:   Mon Jan 30 09:52:25 2023 -0700

    Merge pull request WayScience#38 from jenna-tomkinson/run_plates_with_cp_pipelines

    Run plates with cp pipelines

commit d2b68b7
Author: jenna-tomkinson <jenna.tomkinson@ucdenver.edu>
Date:   Fri Jan 27 12:56:42 2023 -0700

    edit documentation

commit 68e3ded
Author: jenna-tomkinson <jenna.tomkinson@ucdenver.edu>
Date:   Fri Jan 27 09:38:08 2023 -0700

    rerun plate 2 cellprofiler ic to confirm sc count

commit 62dadfa
Author: jenna-tomkinson <jenna.tomkinson@ucdenver.edu>
Date:   Fri Jan 27 09:19:10 2023 -0700

    fix issues wioth extract sc for plate2

commit b3bce04
Author: jenna-tomkinson <jenna.tomkinson@ucdenver.edu>
Date:   Thu Jan 26 15:37:13 2023 -0700

    reorganize repo and run all plates in cp pipelines

commit 347c191
Author: jenna-tomkinson <jenna.tomkinson@ucdenver.edu>
Date:   Tue Jan 24 15:49:47 2023 -0700

    add documentation and converted notebooks

commit 6b917a4
Author: jenna-tomkinson <jenna.tomkinson@ucdenver.edu>
Date:   Tue Jan 24 13:25:07 2023 -0700

    run all plates with cellprofiler pipelines

commit a5221b0
Author: jenna-tomkinson <jenna.tomkinson@ucdenver.edu>
Date:   Mon Jan 23 15:59:10 2023 -0700

    run plate 1 through cp

commit 0ba2392
Merge: 263a94c 310c12f
Author: Jenna Tomkinson <107513215+jenna-tomkinson@users.noreply.github.com>
Date:   Mon Jan 23 11:00:11 2023 -0700

    Merge pull request WayScience#35 from jenna-tomkinson/plate2_cellprofiler

    run plate 2 through cp and extract sc

commit 310c12f
Author: jenna-tomkinson <jenna.tomkinson@ucdenver.edu>
Date:   Mon Jan 23 09:51:03 2023 -0700

    fix red error symbol issue

commit 9404554
Author: jenna-tomkinson <jenna.tomkinson@ucdenver.edu>
Date:   Mon Jan 23 09:39:28 2023 -0700

    save optimized parameters for actin segmenation

commit ec6eb12
Author: jenna-tomkinson <jenna.tomkinson@ucdenver.edu>
Date:   Mon Jan 23 09:18:30 2023 -0700

    run plate 2 through cp and extract sc

commit 263a94c
Merge: a90feed 933a4b1
Author: Jenna Tomkinson <107513215+jenna-tomkinson@users.noreply.github.com>
Date:   Fri Jan 20 12:00:19 2023 -0700

    Merge pull request WayScience#33 from jenna-tomkinson/plate2_illum_correction

    perform IC on plate 2

commit 933a4b1
Author: jenna-tomkinson <jenna.tomkinson@ucdenver.edu>
Date:   Fri Jan 20 11:22:14 2023 -0700

    perform IC on plate 2

commit a90feed
Author: Gregory Way <gregory.way@gmail.com>
Date:   Fri Jan 20 09:15:18 2023 -0700

    DP feature linear modeling and visualization (WayScience#31)

    * perform linear model with DP features

    * add DP visualization for linear model

    * add DP lm figure and small tweak to CP lm fig

    * remove extra empty cell

    * add DP cyto feature power analysis and viz

    * add title to CP power analysis viz

commit 62170be
Author: Gregory Way <gregory.way@gmail.com>
Date:   Fri Jan 20 08:43:01 2023 -0700

    Perform power analysis for CP features (WayScience#30)

    * perform power analysis

    * visualize power analysis

    * visualize top ER feature from KS test (outside scope of PR, sorry!)

    * fix variable name

commit 49fc39a
Author: Gregory Way <gregory.way@gmail.com>
Date:   Fri Jan 20 08:38:29 2023 -0700

    Create umap figure with ggplot (WayScience#29)

    * create umap figure with ggplot

    * add DP figure

commit 77ca026
Merge: 3a615f4 8da9f1c
Author: Jenna Tomkinson <107513215+jenna-tomkinson@users.noreply.github.com>
Date:   Thu Jan 19 15:36:30 2023 -0700

    Merge pull request WayScience#28 from jenna-tomkinson/nf1_dp_statistics

    DeepProfiler data stat analysis

commit 8da9f1c
Author: jenna-tomkinson <jenna.tomkinson@ucdenver.edu>
Date:   Thu Jan 19 15:35:23 2023 -0700

    remove blank figures and edit code

commit 3a615f4
Author: Gregory Way <gregory.way@gmail.com>
Date:   Thu Jan 19 11:28:54 2023 -0700

    Create ComplexHeatmaps for Pilot Data plate 1 (WayScience#27)

    * add notebook to generate complexheatmaps

    * add complex heatmaps

    * add complexheatmap to env

    * save pngs too

    * add pngs and recreate pdfs

commit 0f2e400
Author: jenna-tomkinson <jenna.tomkinson@ucdenver.edu>
Date:   Thu Jan 19 10:58:15 2023 -0700

    DeepProfiler data stat analysis (heatmap and umap)

commit 596e5f7
Author: Gregory Way <gregory.way@gmail.com>
Date:   Thu Jan 19 09:44:06 2023 -0700

    Add linear model analysis (WayScience#26)

    * add code to fit a linear model

    * add linear model results

    * add notebook to visualize linear model results

    * add pycytominer to analyze conda env

    * actually save the figure

    * update figure to show sign

    * remove red symbol

commit 95ecdb6
Author: Gregory Way <gregory.way@gmail.com>
Date:   Wed Jan 18 17:26:48 2023 -0700

    Visualizing the KS test results (WayScience#25)

    * add figure generaetion environment

    * add ks test visualizations

    * add visualization notebook for ks test results

    * get rid of red symbol EOF

    * nbconvert ipynb

    * nbconverting to r instead of python, good catch!

commit e71bb1f
Merge: 1ae36c3 3d18b66
Author: Jenna Tomkinson <107513215+jenna-tomkinson@users.noreply.github.com>
Date:   Wed Jan 18 08:55:10 2023 -0700

    Merge pull request WayScience#23 from jenna-tomkinson/nf1_dp_normalization

    deepprofiler project processing features

commit 3d18b66
Author: jenna-tomkinson <jenna.tomkinson@ucdenver.edu>
Date:   Wed Jan 18 08:50:36 2023 -0700

    edits and update README

commit 46868d3
Author: jenna-tomkinson <jenna.tomkinson@ucdenver.edu>
Date:   Tue Jan 17 15:53:31 2023 -0700

    fix feature selection

commit 3137e54
Author: jenna-tomkinson <jenna.tomkinson@ucdenver.edu>
Date:   Tue Jan 17 15:33:49 2023 -0700

    deeprofiler project processing features

commit 1ae36c3
Merge: 8da88a4 a52b9c7
Author: Jenna Tomkinson <107513215+jenna-tomkinson@users.noreply.github.com>
Date:   Tue Jan 17 11:27:50 2023 -0700

    Merge pull request WayScience#22 from jenna-tomkinson/nf1_analysis

    heatmap and ks-test analysis

commit a52b9c7
Author: jenna-tomkinson <jenna.tomkinson@ucdenver.edu>
Date:   Tue Jan 17 11:27:14 2023 -0700

    edits and add figures

commit f758340
Author: jenna-tomkinson <jenna.tomkinson@ucdenver.edu>
Date:   Tue Jan 17 09:32:01 2023 -0700

    edits

commit ab68cb7
Author: jenna-tomkinson <jenna.tomkinson@ucdenver.edu>
Date:   Fri Jan 13 15:45:52 2023 -0700

    heatmap and ks-test analysis

commit 8da88a4
Merge: 610854c 283d170
Author: Jenna Tomkinson <107513215+jenna-tomkinson@users.noreply.github.com>
Date:   Wed Jan 11 11:05:31 2023 -0700

    Merge pull request WayScience#21 from jenna-tomkinson/nf1_statistics

    NF1 UMAP Stats

commit 283d170
Author: jenna-tomkinson <jenna.tomkinson@ucdenver.edu>
Date:   Wed Jan 11 11:00:48 2023 -0700

    edit plot of number of sc

commit ec78e8c
Author: jenna-tomkinson <jenna.tomkinson@ucdenver.edu>
Date:   Wed Jan 11 10:10:43 2023 -0700

    improved code to remove extra lines

commit 08bbb0f
Author: jenna-tomkinson <jenna.tomkinson@ucdenver.edu>
Date:   Tue Jan 10 15:54:06 2023 -0700

    complete review edits

commit 74d1917
Author: jenna-tomkinson <jenna.tomkinson@ucdenver.edu>
Date:   Mon Jan 9 15:19:21 2023 -0700

    UMAP notebooks and visualizations

commit 9adc2b4
Author: jenna-tomkinson <jenna.tomkinson@ucdenver.edu>
Date:   Fri Jan 6 15:43:45 2023 -0700

    add notebook for sc counts

commit 5782633
Author: jenna-tomkinson <jenna.tomkinson@ucdenver.edu>
Date:   Fri Jan 6 15:41:31 2023 -0700

    start of NF1 statistics

commit 610854c
Merge: 1e70c20 b7bec10
Author: Jenna Tomkinson <107513215+jenna-tomkinson@users.noreply.github.com>
Date:   Wed Dec 14 14:13:53 2022 -0700

    Merge pull request WayScience#19 from jenna-tomkinson/add_new_dataset

    Add second NF1 dataset and correct the images

commit b7bec10
Author: jenna-tomkinson <jenna.tomkinson@ucdenver.edu>
Date:   Wed Dec 14 14:08:04 2022 -0700

    fix barcode platemap

commit ab702df
Author: jenna-tomkinson <jenna.tomkinson@ucdenver.edu>
Date:   Wed Dec 14 11:09:49 2022 -0700

    update .py file

commit 17fa768
Author: jenna-tomkinson <jenna.tomkinson@ucdenver.edu>
Date:   Wed Dec 14 11:06:52 2022 -0700

    update code and run second plate

commit 8d90300
Author: jenna-tomkinson <jenna.tomkinson@ucdenver.edu>
Date:   Tue Dec 13 14:50:50 2022 -0700

    add updated dataset (from 12/12) and edit code

commit c6bf525
Author: jenna-tomkinson <jenna.tomkinson@ucdenver.edu>
Date:   Mon Dec 12 15:54:05 2022 -0700

    updating code

commit ec3321c
Author: jenna-tomkinson <jenna.tomkinson@ucdenver.edu>
Date:   Fri Dec 9 16:50:49 2022 -0700

    update main README

commit a6b9987
Author: jenna-tomkinson <jenna.tomkinson@ucdenver.edu>
Date:   Fri Dec 9 16:49:38 2022 -0700

    update main README

commit a073b94
Author: jenna-tomkinson <jenna.tomkinson@ucdenver.edu>
Date:   Fri Dec 9 16:40:58 2022 -0700

    edits from review

commit 0d0b2cb
Author: jenna-tomkinson <jenna.tomkinson@ucdenver.edu>
Date:   Fri Dec 9 09:33:59 2022 -0700

    add black format to .py file

commit 23209b0
Author: jenna-tomkinson <jenna.tomkinson@ucdenver.edu>
Date:   Fri Dec 9 09:31:37 2022 -0700

    edit the documentation in the .py file

commit a3cb4b5
Author: jenna-tomkinson <jenna.tomkinson@ucdenver.edu>
Date:   Fri Dec 9 09:06:08 2022 -0700

    edit README

commit 6c878e5
Author: jenna-tomkinson <jenna.tomkinson@ucdenver.edu>
Date:   Fri Dec 9 08:56:38 2022 -0700

    edit README

commit 3a928d2
Author: jenna-tomkinson <jenna.tomkinson@ucdenver.edu>
Date:   Thu Dec 8 18:08:13 2022 -0700

    edit notebook

commit da69b4e
Author: jenna-tomkinson <jenna.tomkinson@ucdenver.edu>
Date:   Thu Dec 8 18:02:36 2022 -0700

    small edits to .py file

commit ed150bc
Author: jenna-tomkinson <jenna.tomkinson@ucdenver.edu>
Date:   Thu Dec 8 18:01:48 2022 -0700

    corrected metadata and finished code

commit 8e855e0
Author: jenna-tomkinson <jenna.tomkinson@ucdenver.edu>
Date:   Thu Dec 8 17:44:04 2022 -0700

    update data and reordered the metadata

commit 6fd34de
Author: jenna-tomkinson <jenna.tomkinson@ucdenver.edu>
Date:   Tue Dec 6 14:27:31 2022 -0700

    add second plate

commit 1e70c20
Merge: 5536d86 861d71b
Author: Jenna Tomkinson <107513215+jenna-tomkinson@users.noreply.github.com>
Date:   Mon Nov 28 13:06:10 2022 -0700

    Merge pull request WayScience#17 from jenna-tomkinson/edit_features_module

    Edit 4_processing_features module

commit 861d71b
Author: jenna-tomkinson <jenna.tomkinson@ucdenver.edu>
Date:   Mon Nov 28 13:04:49 2022 -0700

    edits

commit 1c8d46d
Author: jenna-tomkinson <jenna.tomkinson@ucdenver.edu>
Date:   Mon Nov 28 12:51:42 2022 -0700

    edits

commit be76e1b
Author: jenna-tomkinson <jenna.tomkinson@ucdenver.edu>
Date:   Mon Nov 28 12:50:06 2022 -0700

    edited documentation

commit cb7f39f
Author: jenna-tomkinson <jenna.tomkinson@ucdenver.edu>
Date:   Mon Nov 28 09:45:35 2022 -0700

    edited instructions and added file

commit 39f1bb0
Author: jenna-tomkinson <jenna.tomkinson@ucdenver.edu>
Date:   Mon Nov 14 14:32:25 2022 -0700

    correct metadata to rerun dp module

commit df7cedd
Author: jenna-tomkinson <jenna.tomkinson@ucdenver.edu>
Date:   Mon Nov 14 13:54:50 2022 -0700

    updated main README

commit 7c26bd6
Author: jenna-tomkinson <jenna.tomkinson@ucdenver.edu>
Date:   Mon Nov 14 13:51:13 2022 -0700

    edit data and create readme
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