Advanced Usage introduction simplification
#378
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Would it make more sense to discuss these changes by creating a new template file specifically for advanced topics? I guess this is a good way to get the conversation started. |
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| <img src="https://github.com/AlexsLemonade/refinebio-examples/raw/40e47f4d3f39283effbd9843a457168061be9680/template/screenshots/download-email.png" width=500> | ||
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| We are going to use non-quantile normalized data for this analysis. |
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I'm worried about deleting this piece in particular. We need them to know whether or not they should download quantile normalized data and where to find that.
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I do cover that on line 40, but it could be made more prominent.
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I think screenshots help. I guess bigger question is just because someone's an "advanced topics" user, can we assume they know how to download data from refine.bio and know the refine.bio options more readily?
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I guess I think even advanced topics users will appreciate screenshots. Though I do agree with cutting back on the file path hand holding.
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That was my thought, or they could go to another example to get this information. 🤷🏼
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go to another example to get this information. 🤷🏼
If we think they might do this, then we should probably just keep the screenshots here too. I think screenshots help decrease brain glucose usage for simple things.
That is what #372 is for. We split up making the first example from a general template. |
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Converting this to a draft pending incorporation of changes in #379 |
Other changes will come with merging in data section.
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Couple other comments in the meantime.
I still disagree with getting rid of the screenshots. I don't think "advanced users" will be upset by having more screenshots. But perhaps we can ask Deepa to weigh in on a discussion about what different kinds of users might expect or respond.
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| Clicking this link will most likely send this to your downloads folder on your computer. | ||
| Move this `.Rmd` file to where you would like this example and its files to be stored. | ||
| To run this example yourself, [download the `.Rmd` for this analysis by clicking this link](https://alexslemonade.github.io/refinebio-examples/03-rnaseq/differential_expression_rnaseq_01_rnaseq.Rmd) and moving the `.Rmd` file to your preferred analysis folder. |
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| To run this example yourself, [download the `.Rmd` for this analysis by clicking this link](https://alexslemonade.github.io/refinebio-examples/03-rnaseq/differential_expression_rnaseq_01_rnaseq.Rmd) and moving the `.Rmd` file to your preferred analysis folder. | |
| To run this example yourself, [download the `.Rmd` for this analysis by clicking this link](https://alexslemonade.github.io/refinebio-examples/03-rnaseq/differential_expression_rnaseq_01_rnaseq.Rmd) and move the `.Rmd` file to your preferred analysis folder. |
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| <img src="https://github.com/AlexsLemonade/refinebio-examples/raw/40e47f4d3f39283effbd9843a457168061be9680/template/screenshots/download-email.png" width=500> | ||
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| We are going to use non-quantile normalized data for this analysis. |
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go to another example to get this information. 🤷🏼
If we think they might do this, then we should probably just keep the screenshots here too. I think screenshots help decrease brain glucose usage for simple things.
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| # Create the plots folder if it doesn't exist | ||
| if (!dir.exists(plots_dir)) { | ||
| dir.create(plots_dir) |
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We still will need to create these directories though. (Unless you've put this part somewhere else)
Purpose
This PR is to try out some simplifiedsetup instructions for advanced use examples. The general idea is that if people are clicking on "advanced" then they might not need quite so detailed instructions for the introduction
Issue addressed
Closes #357
Remaining concerns and questions
The main question the reviewers should address is whether these instructions are sufficiently clear for someone who comes in with a bit more knowledge of the material; i.e. someone who has used refine.bio before to download data files and has done at least one R notebook analysis.
Additionally, is there enough of an off-ramp for someone who comes in without the prior knowledge... is there enough detail about where to go for more detailed instructions?