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Clarify datasets #36

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Nov 4, 2022
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Clarify datasets #36

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Add dataset table
shntnu Nov 2, 2022
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shntnu Nov 2, 2022
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Add table + formatting
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3 changes: 0 additions & 3 deletions 1.run-workflows/profiles/NCP_PROGENITORS_1/BR_NCP_PROGENITORS_1.csv.gz
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3 changes: 0 additions & 3 deletions 1.run-workflows/profiles/NCP_PROGENITORS_1_BRANCHING/BR_NCP_PROGENITORS_1.csv.gz
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59 changes: 38 additions & 21 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -16,37 +16,55 @@
There are 48 IPSC lines available for this project from the [22q cohort](https://docs.google.com/spreadsheets/d/1ShXDddzO5mK7-C6G_BQYM3H7y8-2sGOOUn5uRX6SXVk/edit#gid=0):


|Metadata_line_source |Metadata_line_condition | n|
|:--------------------|:-----------------------|--:|
|human |control | 22|
|human |deletion | 22|
|isogenic_control |control | 2|
|isogenic_deletion |deletion | 2|

Profiles from newer datasets (2022 onwards) are in this data repo https://github.com/broadinstitute/2019_05_28_Neuronal_Cell_Painting
| Metadata_line_source | Metadata_line_condition | n |
| :------------------- | :---------------------- | ---: |
| human | control | 22 |
| human | deletion | 22 |
| isogenic_control | control | 2 |
| isogenic_deletion | deletion | 2 |

<details>
<summary> Code </summary>

```r
read_tsv("metadata/NCP_STEM_1/platemap/BR_NCP_STEM_1.txt") %>%
distinct(line_ID, line_condition, line_source) %>% count(line_source, line_condition) %>%
read_tsv("metadata/NCP_STEM_1/platemap/BR_NCP_STEM_1.txt") %>%
distinct(line_ID, line_condition, line_source) %>% count(line_source, line_condition) %>%
knitr::kable()
```

</details>

TODO: All this information should be moved to the [Project Profiler airtable](https://airtable.com/appctUGldmRNkVS19/tblXX3mTxhCR9Bxbq/viwNJfGOOJot7Wr3x?blocks=hide).
TODO: Fill in information about number of features

| Experiment | Plate | Features | Magnification | Profiles | Notes |
| ---------------------------- | ---------------- | ---------------------- | ------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------- | --------------------------------------------------------------------------------------------------------------------------------------------------- |
| NCP Stem 1 | BR\_NCP\_STEM\_1 | Cell Painting (n=4293) | 20x | [GitHub](1.run-workflows/profiles/NCP_STEM_1/BR_NCP_STEM_1) | |
| NCP Progenitor 1 | BR00127194 | Cell Painting (n=4295) | 20x | [GitHub](1.run-workflows/profiles/NCP_PROGENITORS_1/BR00127194) | This is a repeat of an experiment that failed ([notes)](https://github.com/broadinstitute/neuronal-cell-painting/issues/10#issuecomment-909397555). |
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| NCP Neuron 1 - Cell Painting | BR00132672 | | 20x | [S3](https://imaging-platform.s3.amazonaws.com/projects/2019_05_28_Neuronal_Cell_Painting/workspace/profiles/2022_03_03_NCP_NEURONS_2_20x/BR00132672) | ([notes](https://github.com/broadinstitute/neuronal-cell-painting/issues/21#issuecomment-1077803763)) |
| NCP Neuron 1 - Cell Painting | BR00132672 | | 63x | [S3](https://imaging-platform.s3.amazonaws.com/projects/2019_05_28_Neuronal_Cell_Painting/workspace/profiles/2022_03_03_NCP_NEURONS_2_63x/BR00132672) | same ^^^ |
| NCP Neuron 1 - Cell Painting | BR00132673 | | 20x | [S3](https://imaging-platform.s3.amazonaws.com/projects/2019_05_28_Neuronal_Cell_Painting/workspace/profiles/2022_03_03_NCP_NEURONS_2_20x/BR00132673) | same ^^^ |
| NCP Neuron 1 - Cell Painting | BR00132673 | | 63x | [S3](https://imaging-platform.s3.amazonaws.com/projects/2019_05_28_Neuronal_Cell_Painting/workspace/profiles/2022_03_03_NCP_NEURONS_2_63x/BR00132673) | same ^^^ |

Failed experiments

| Experiment | Plate | Features | Profiles | Notes |
| ---------------- | ----------------------- | ---------------------- | ----------------------------------------------------------------------------------- | --------------------------------------------------------------------------------------------------------------------------------------------- |
| NCP Progenitor 1 | BR\_NCP\_PROGENITORS\_1 | Cell Painting (n=4293) | [GitHub](1.run-workflows/profiles/NCP_PROGENITORS_1/BR_NCP_PROGENITORS_1) | This was the first attempt but it failed ([notes](https://github.com/broadinstitute/neuronal-cell-painting/issues/10#issuecomment-740777303)) |
| | BR\_NCP\_PROGENITORS\_1 | Branching (n=23) | [GitHub](1.run-workflows/profiles/NCP_PROGENITORS_1_BRANCHING/BR_NCP_PROGENITORS_1) | Same as above, only branching metrics |


Profiles from newer datasets (2022 onwards) are in this data repo https://github.com/broadinstitute/2019_05_28_Neuronal_Cell_Painting

We have RNA-Seq data (Nehme, Pietiläinen, et al., submitted) for 20 healthy controls and 28 patients with 22q deletion, across 3 stages:

- D0 (undifferentiated stem cells)
- D4 (progenitors, with GFP)
- D28 (neurons)

## Experiment schedule

- D0 experiment completed
- D4 experiment completed
- D0 experiment completed
- D4 experiment completed
- D28 experiment estimated to be done 2021-10-7

## Computational environment
Expand Down Expand Up @@ -74,10 +92,10 @@ conda activate pooled-cell-painting-analysis

### R

We use [`renv`](https://rstudio.github.io/renv/index.html) to reproduce R code.
We use [`renv`](https://rstudio.github.io/renv/index.html) to reproduce R code.
We recommend using RStudio as your IDE.

Checkout this repository and then load the project `neuronal-cell-painting.Rproj` in RStudio.
Checkout this repository and then load the project `neuronal-cell-painting.Rproj` in RStudio.
You should see this

```
Expand All @@ -92,13 +110,13 @@ You should see this

Now run `renv::restore()` and you're ready to run the R scripts in this repo.

Note: If you end up with issues with compiling libraries and you are on OSX, it's probably something to do with the macOS toolchain for versions of R starting at 4.y.z. being broken.
Note: If you end up with issues with compiling libraries and you are on OSX, it's probably something to do with the macOS toolchain for versions of R starting at 4.y.z. being broken.
Follow these [instructions](https://thecoatlessprofessor.com/programming/cpp/r-compiler-tools-for-rcpp-on-macos/) to get set up.

#### Creating a new R notebook

Here's an example directory structure for a directory `<project>/<module-name>` containing an R notebook.
Note that R and Python notebooks can co-exist in the same directory
Note that R and Python notebooks can co-exist in the same directory

```
<module-name>/
Expand All @@ -112,10 +130,9 @@ Note that R and Python notebooks can co-exist in the same directory

Here are the steps to follow to create add such a notebook to this repo

- Create a stub for `1.inspect-data.Rmd`
- Create a stub for `1.inspect-data.Rmd`
- Copy [`_output.yaml`](https://gist.github.com/shntnu/12f5124fc0b8d9fbcef2765b89af9668) and [`0.knit-notebooks.R`](https://gist.github.com/shntnu/db9794e3d2ffbed09e290ffbb150512f) into the directory if it does not already exist
- Create a directory `knit_notebooks`; this is where the rendered versions of the notebooks will live
- Edit `0.knit-notebooks.R` to add `render_notebook("1.inspect-cp221")`, which will render this notebook in markdown int the `knit_notebooks` directory
- Now continue doing your analysis in `1.inspect-cp221.Rmd` and run things interactively as you would
- When its time to commit, generate the markdown for the notebook by running `0.knit-notebooks.R`. Ensure that your current working directory is the parent directory of `0.knit-notebooks.R` before doing so. As you add more notebooks to the directory, `0.knit-notebooks.R` will have more entries in it, but you may want to only render your latest notebook. In this case, you'd need to run things by hand: first run the function definition for `render_notebook()` and then run `render_notebook("1.inspect-data")`. This will render the file `1.inspect-data.md` along with the figures in `1.inspect-data_files`. You should commit all of this to the repo.
-