fixing images that caused hidden info

Author: carriewright11

05-scientific-notebooks.Rmd

@@ -56,29 +56,29 @@ Because of all of these reasons, we encourage the use of computational notebooks
 [Click this link to download](https://raw.githubusercontent.com/jhudsl/Reproducibility_in_Cancer_Informatics/main/chapter-zips/python-heatmap-chapt-5.zip).
 
 ```{bash, include = FALSE}
-mkdir -p chapter-zips
-wget -O chapter-zips/python-heatmap-chapt-5.zip https://raw.githubusercontent.com/jhudsl/Reproducibility_in_Cancer_Informatics/main/chapter-zips/python-heatmap-chapt-5.zip
+#mkdir -p chapter-zips
+#wget -O chapter-zips/python-heatmap-chapt-5.zip https://raw.githubusercontent.com/jhudsl/Reproducibility_in_Cancer_Informatics/main/chapter-zips/python-heatmap-chapt-5.zip
 ```
 
 Now double click your chapter zip file to unzip. For Windows you may have to [follow these instructions](https://support.microsoft.com/en-us/windows/zip-and-unzip-files-f6dde0a7-0fec-8294-e1d3-703ed85e7ebc).
 
 ```{bash, include = FALSE}
-unzip -o chapter-zips/python-heatmap-chapt-5.zip -d chapter-zips/
+#unzip -o chapter-zips/python-heatmap-chapt-5.zip -d chapter-zips/
 ```
 </details>
 
 <details> <summary>**Get the R project example files**</summary>
 [Click this link to download](https://raw.githubusercontent.com/jhudsl/Reproducibility_in_Cancer_Informatics/main/chapter-zips/r-heatmap-chapt-5.zip).
 
 ```{bash, include = FALSE}
-mkdir -p chapter-zips
-wget -O chapter-zips/r-heatmap-chapt-5.zip https://raw.githubusercontent.com/jhudsl/Reproducibility_in_Cancer_Informatics/main/chapter-zips/r-heatmap-chapt-5.zip
+#mkdir -p chapter-zips
+#wget -O chapter-zips/r-heatmap-chapt-5.zip https://raw.githubusercontent.com/jhudsl/Reproducibility_in_Cancer_Informatics/main/chapter-zips/r-heatmap-chapt-5.zip
 ```
 
 Now double click your chapter zip file to unzip. For Windows you may have to [follow these instructions](https://support.microsoft.com/en-us/windows/zip-and-unzip-files-f6dde0a7-0fec-8294-e1d3-703ed85e7ebc).
 
 ```{bash, include = FALSE}
-unzip -o chapter-zips/r-heatmap-chapt-5.zip -d chapter-zips/
+#unzip -o chapter-zips/r-heatmap-chapt-5.zip -d chapter-zips/
 ```
 </details>
 
@@ -165,11 +165,13 @@ Now, in your respective IDE, we'll turn our unreproducible scripts into notebook
 1. Start a new notebook by going to `New` > `Notebook`.
 2. Then open up this chapter’s example code folder and open the `make-heatmap.py` file.
 
-<img src ="https://docs.google.com/presentation/d/1LMurysUhCjZb7DVF6KS9QmJ5NBjwWVjRn40MS9f2noE/export/png?id=1LMurysUhCjZb7DVF6KS9QmJ5NBjwWVjRn40MS9f2noE&pageid=gfaa026a583_0_20" alt="In Jupyter, you can create a new notebook by going to New > Notebook. Then open up this chapter’s example code folder and open the make-heatmap.py file." style="display: block; margin: auto;" />
+<img src ="https://docs.google.com/presentation/d/1LMurysUhCjZb7DVF6KS9QmJ5NBjwWVjRn40MS9f2noE/export/png?id=1LMurysUhCjZb7DVF6KS9QmJ5NBjwWVjRn40MS9f2noE&pageid=gfaa026a583_0_20" alt="In Jupyter, you can create a new notebook by going to New then Notebook. Then open up this chapter’s example code folder and open the make-heatmap.py file."  />
+
 
 3. Create a new code chunk in your notebook.
 
-<img src ="https://docs.google.com/presentation/d/1LMurysUhCjZb7DVF6KS9QmJ5NBjwWVjRn40MS9f2noE/export/png?id=1LMurysUhCjZb7DVF6KS9QmJ5NBjwWVjRn40MS9f2noE&pageid=gfaa026a583_0_30" alt="The Jupyter interface has a ‘add a new chunk’ button, a delete chunk button, and a dropdown menu that allows you to choose the chunk type you’d like to add." style="display: block; margin: auto;" />
+
+<img src ="https://docs.google.com/presentation/d/1LMurysUhCjZb7DVF6KS9QmJ5NBjwWVjRn40MS9f2noE/export/png?id=1LMurysUhCjZb7DVF6KS9QmJ5NBjwWVjRn40MS9f2noE&pageid=gfaa026a583_0_30" alt="The Jupyter interface has a ‘add a new chunk’ button, a delete chunk button, and a dropdown menu that allows you to choose the chunk type you’d like to add." />
 
 
 4. Now copy and paste all of the code from `make-heatmap.py` into a new chunk. We will later break up this large chunk of code into smaller chunks that are thematic in the next chapter.
@@ -182,26 +184,35 @@ For [more about using Jupyter notebooks see this](https://realpython.com/jupyter
 <details> <summary>**Set up an R notebook**</summary>
 
 1. Start a new notebook by going to `File` > `New File` > `R Notebook`.
-2. Then open up this chapter’s example code folder and open the `make_heatmap.R` file.
 
-<img src ="https://docs.google.com/presentation/d/1LMurysUhCjZb7DVF6KS9QmJ5NBjwWVjRn40MS9f2noE/export/png?id=1LMurysUhCjZb7DVF6KS9QmJ5NBjwWVjRn40MS9f2noE&pageid=gfaa026a583_0_13" alt="In RStudio, you can create a new notebook by going to File > New File > R Notebook. Then open up this chapter’s example code folder and open the make_heatmap.R file." style="display: block; margin: auto;" />
+<img src ="https://docs.google.com/presentation/d/1LMurysUhCjZb7DVF6KS9QmJ5NBjwWVjRn40MS9f2noE/export/png?id=1LMurysUhCjZb7DVF6KS9QmJ5NBjwWVjRn40MS9f2noE&pageid=gfaa026a583_0_13" alt="In RStudio, you can create a new notebook by going to File then New File then R Notebook. Then open up this chapter’s example code folder and open the make_heatmap.R file." />
 
+2. Then open up this chapter’s example code folder and open the `make_heatmap.R` file.
 3. Practice creating a new chunk in your R notebook by clicking the `Code` > `Insert Chunk` button on the toolbar or by pressing `Cmd+Option+I` (in Mac) or `Ctrl + Alt + I` (in Windows). (You can also manually type out the back ticks and `{}`)  
 4. Delete all the default text in this notebook but keep the header which is surrounded by `---` and looks like:  
+
 `````
 title: "R Notebook"
 output: html_notebook
 `````
-You can feel free to change the title from `R Notebook` to something that better suits the contents of this notebook.  
+You can feel free to change the title from `R Notebook` to something that better suits the contents of this notebook. 
+
 5. Now copy and paste all of the code from `make_heatmap.R` into a new chunk. We will later break up this large chunk of code into smaller chunks that are thematic in the next chapter.   
 6. Save your `untitled.Rmd` into something that tells us what it will end up doing like `make-heatmap.Rmd`.  
 7. Notice that upon saving your `.Rmd` file, a new file `.nb.html` file of the same name is created. Open that file and choose `view in Browser`. If RStudio asks you to choose a browser, then choose a default browser.  
 8. This shows the nicely rendered version of your analysis and snapshots whatever output existed when the `.Rmd` file was saved.  
 
 For [more about using R notebooks see this](https://bookdown.org/yihui/rmarkdown/) by @Xie2018.
 
+
+
+
 </details>
 
+
+<br>
+<br>
+
 Now that you've created your notebook, you are ready to start polishing that code!
 
 **Any feedback you have regarding this exercise is greatly appreciated; you can fill out [this form](https://forms.gle/ygSSwoGaEATA2S65A)!**