Merge pull request #8 from GenomicsAotearoa/revisions_022024

Revisions 022024

docs/02-data-prelude.md

@@ -1,8 +1,8 @@
 # Introduction to the example dataset and file type
 
-!!! info 
+!!! info "Learning outcomes"
 
-    === "Keypoints"
+    === "Key points"
 
         - The dataset comes from a real world experiment in *E. coli*.
         - Publicly available FASTQ files can be downloaded from NCBI SRA.

docs/07-knitr-markdown.md

@@ -2,7 +2,7 @@
 
 !!! info 
 
-    === "Keypoints"
+    === "Key points"
 
         - Keep reporting and R software together in one document using R
           Markdown.
@@ -51,14 +51,14 @@ can just re-compile the report and get the new or corrected results
 (versus having to reconstruct figures, paste them into a Word document,
 and further hand-edit various detailed results).
 
-The key tool for R is [knitr](http://yihui.name/knitr/), which allows
+The key tool for R is [`knitr`](http://yihui.name/knitr/), which allows
 you to create a document that is a mixture of text and some chunks of
-code. When the document is processed by knitr, chunks of R code will be
+code. When the document is processed by `knitr`, chunks of R code will be
 executed, and graphs or other results inserted.
 
 This sort of idea has been called "literate programming".
 
-knitr allows you to mix basically any sort of text with any sort of
+`knitr` allows you to mix basically any sort of text with any sort of
 code, but we recommend that you use R Markdown, which mixes Markdown
 with R. Markdown is a light-weight mark-up language for creating web
 pages.
@@ -68,9 +68,7 @@ pages.
 Within R Studio, click File → New File → R Markdown and you'll get a
 dialog box like this:
 
-<!-- Need to generate the image.
-![images]()
--->
+![Alt text](figures/open_new_Rmd.png)
 
 You can stick with the default (HTML output), but give it a title.
 
@@ -185,7 +183,7 @@ You can make a hyperlink like this:
 You can include an image file like this:
 `![caption](http://url/for/file)`
 
-You can do subscripts (e.g., F~2~) with `F~2` and superscripts (e.g.,
+You can do subscripts (e.g., F~2~) with `F~2~` and superscripts (e.g.,
 F^2^) with `F^2^`.
 
 If you know how to write equations in

docs/08-r-help.md

@@ -2,7 +2,7 @@
 
 !!! info 
 
-    === "Keypoints"
+    === "Key points"
 
         - R provides thousands of functions for analyzing data, and provides several way to get help
         - Using R will mean searching for online help, and there are tips and resources on how to search effectively
@@ -55,10 +55,10 @@ Often, in order to duplicate the issue you are having, someone may need
 to see the data you are working with or verify the versions of R or R
 packages you are using. The following R functions will help with this:
 
-You can **check the version of R** you are working with using the
-`sessionInfo()` function. Actually, it is good to save this information
-as part of your notes on any analysis you are doing. When you run the
-same script that has worked fine a dozen times before, looking back at
+You can **check the version of R** (and any loaded packages) you are working 
+with using the `sessionInfo()` function. Actually, it is good to save this 
+information as part of your notes on any analysis you are doing. When you run 
+the same script that has worked fine a dozen times before, looking back at
 these notes will remind you that you upgraded R and forget to check your
 script.
 
@@ -91,12 +91,11 @@ script.
 Many times, there may be some issues with your data and the way it is
 formatted. In that case, you may want to share that data with someone
 else. However, you may not need to share the whole dataset; looking at a
-subset of your 50,000 row, 10,000 column dataframe may be TMI (too much
-information)! You can take an object you have in memory such as
-dataframe (if you don't know what this means yet, we will get to it!)
-and save it to a file. In our example we will use the `dput()` function
-on the `iris` dataframe which is an example dataset that is installed in
-R:
+subset of your 50,000 row, 10,000 column data frame may be TMI (too much
+information)! You can take an object you have in memory such as a
+data frame and save it to a file. In our example we will use the `dput()` 
+function on the `iris` data frame which is an example dataset that is installed 
+in R:
 
 !!! r-project "r"
 
@@ -163,15 +162,15 @@ them here because they come up commonly:
     1:101 # generates the sequence of numbers from 1 to 101
     ```
 
-!!! success "Output"
-
-    ```
-      [1]   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  19  20  21  22
-     [23]  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38  39  40  41  42  43  44
-     [45]  45  46  47  48  49  50  51  52  53  54  55  56  57  58  59  60  61  62  63  64  65  66
-     [67]  67  68  69  70  71  72  73  74  75  76  77  78  79  80  81  82  83  84  85  86  87  88
-     [89]  89  90  91  92  93  94  95  96  97  98  99 100 101
-    ```
+    !!! success "Output"
+    
+        ```
+          [1]   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  19  20  21  22
+         [23]  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38  39  40  41  42  43  44
+         [45]  45  46  47  48  49  50  51  52  53  54  55  56  57  58  59  60  61  62  63  64  65  66
+         [67]  67  68  69  70  71  72  73  74  75  76  77  78  79  80  81  82  83  84  85  86  87  88
+         [89]  89  90  91  92  93  94  95  96  97  98  99 100 101
+        ```
 
 In the output above, `[89]` indicates that the first value on that line
 is the 89th item in your result

docs/appendix/04-bioconductor-vcfr.md

@@ -2,7 +2,7 @@
 
 !!! info 
 
-    === "Keypoints"
+    === "Keyp oints"
 
         - Bioconductor is an alternative package repository for bioinformatics packages.
         - Installing packages from Bioconductor requires a new method, since it is not compatible with the `install.packages()` function used for CRAN.