Merge pull request #6 from fhdsl/lesson1

Lesson1
fhdsl · Sep 28, 2023 · fb7ff69 · fb7ff69
2 parents 1188505 + fc83c0a
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diff --git a/01-intro.Rmd b/01-intro.Rmd
@@ -13,7 +13,3 @@ The course is intended for researchers who want to learn coding for the first ti
 
 The course covers fundamentals of R, a high-level programming language, and use it to wrangle data for analysis and visualization. The programming skills you will learn are transferable to learn more about R independently and other high-level languages such as Python. At the end of the class, you will be reproducing analysis from a scientific publication!
 
-
-```{r}
-devtools::session_info()
-```
diff --git a/lesson1.Rmd → 02-lesson1.Rmd b/lesson1.Rmd → 02-lesson1.Rmd
@@ -1,16 +1,7 @@
-
-# A new chapter
-
-If you haven't yet read the getting started Wiki pages; [start there](https://www.ottrproject.org/getting_started.html).
-
-To see the rendered version of this chapter and the rest of the template, see here: https://jhudatascience.org/OTTR_Template/.
-
-Every chapter needs to start out with this chunk of code:
-
-
 ```{r, include = FALSE}
 ottrpal::set_knitr_image_path()
 ```
+
 # W1: Intro to Computing
 
 ## Goals of the course
@@ -141,7 +132,7 @@ x = 18 + 21
 
 If you enter this in the Console, you will see that in the Environment, the variable `x` has a value of `39`.
 
-::: {.callout-tip}
+::: callout-tip
 ## Execution rule for variable assignment
 
 Evaluate the expression to the right of `=`.
@@ -168,7 +159,7 @@ y = x * 2
 
 A function has a **function name**, **arguments**, and **returns** a data type.
 
-::: {.callout-tip}
+::: callout-tip
 ## Execution rule for functions:
 
 Evaluate the function by its arguments, and if the arguments are functions or contains operations, evaluate those functions or operations first.
@@ -214,13 +205,10 @@ Common errors:
 
 -   It did something else than I expected!
 
-
 Solutions:
 
 -   Where is the problem?
 
 -   What kind of problem is it?
 
 -   Explain your problem to someone!
-
-
diff --git a/_bookdown.yml b/_bookdown.yml
@@ -1,9 +1,8 @@
 book_filename: "Season 1 Introduction to R"
 chapter_name: "Chapter "
 repo: https://github.com/jhudsl/OTTR_Template/
-rmd_files: ["index.Rmd",
-            "01-intro.Rmd",
-            "lesson1.Rmd",
+rmd_files: ["01-intro.Rmd",
+            "02-lesson1.Rmd",
             "About.Rmd",
             "References.Rmd"]
 new_session: yes

diff --git a/_output.yml b/_output.yml
@@ -1,15 +1,16 @@
 bookdown::gitbook:
   css: assets/style.css
   includes:
-    before_body: assets/big-image.html
+    before_body: assets/big-image_fhdasl.html
     after_body: assets/footer.html
   highlight: tango
   config:
     toc:
       collapse: section
       before: |
-       <a href="http://jhudatascience.org/"><img src="https://jhudatascience.org/images/dasl.png" style=" width: 80%; padding-left: 40px; padding-top: 8px; vertical-align: top "</a>
+       <a href="https://hutchdatascience.org/" target="_blank"><img src="assets/big-dasl-stacked.png" style="width: 80%; padding-left: 34px; padding-top: 8px;"</a>
       after: |
-       <p style="text-align:center;"> <a href="https://github.com/jhudsl/OTTR_Template" target="blank" > This content was published with</a> <a href="https://bookdown.org/" target="blank"> bookdown by:</a> </p>
-       <p style="text-align:center;"> <a href="http://jhudatascience.org/"> The Johns Hopkins Data Science Lab </a></p>
+       <p style="text-align:center;"> <a href="https://github.com/jhudsl/OTTR_Template" target="blank" > This content was published with</a> <a href="https://bookdown.org/" target="blank"> bookdown by: </a> </p>
+       <p style="text-align:center;"> <a href="https://hutchdatascience.org/"> The Fred Hutch Data Science Lab </a></p>
        <p style="text-align:center; font-size: 12px;"> <a href="https://github.com/rstudio4edu/rstudio4edu-book/"> Style adapted from: rstudio4edu-book </a> <a href ="https://creativecommons.org/licenses/by/2.0/"> (CC-BY 2.0) </a></p>
+       <p style="padding-left: 40px;"><div class="trapezoid" style = "padding-left: 40px;"><span>  <a href="https://forms.gle/W6Mg4rzuMK6Yk3Am8"> Click here to provide feedback</a> <img src="assets/itcr_arrow.png" style=" width: 10%" ></span></div></p>
diff --git a/classroom_data/CCLE.RData b/classroom_data/CCLE.RData
diff --git a/classroom_data/CCLE_metadata.csv b/classroom_data/CCLE_metadata.csv
diff --git a/classroom_data/gen_classroom_data.R b/classroom_data/gen_classroom_data.R
@@ -0,0 +1,36 @@
+library(tidyverse)
+
+#Raw data downloaded from https://depmap.org/portal/download/all/. 
+#Raw data too large to keep in repository. 
+metadata = read.csv("../DepMap_23Q2_raw/Model.csv")
+mutation = read.csv("../DepMap_23Q2_raw/OmicsSomaticMutations.csv")
+expression = read.csv("../DepMap_23Q2_raw/OmicsExpressionProteinCodingGenesTPMLogp1.csv")
+
+
+#Simplify mutation data for classroom use
+#Pick genes that are Cosmic Hotspot, Driver, LikelyDriver, LoF
+#Description of these criteria found https://storage.googleapis.com/shared-portal-files/Tools/%5BDMC%20Communication%5D%2022Q4%20Mutation%20Pipeline%20Update.pdf
+mutation = summarise(group_by(mutation, ModelID, HugoSymbol),
+                            mutated = ifelse(length(which(CosmicHotspot == "True" | 
+                                                          Driver == "True" | LoF == "True" |
+                                                          LikelyDriver == "True")) >= 1, TRUE, NA))
+mutation = pivot_wider(mutation, names_from = "HugoSymbol", values_from = "mutated")
+
+idx = apply(mutation, MARGIN = 2, function(x) !all(is.na(x)))
+mutation = mutation[, idx]
+mutation[is.na(mutation)] = FALSE
+
+#Clean up expression data
+colnames(expression) = gsub("(.*)\\.\\..*", "\\1", colnames(expression)) 
+#Subset expression data to be close to mutation data.
+idx = c(1, which(colnames(expression) %in% colnames(mutation)))
+expression = expression[, idx]
+
+#Clean up colnames in mutation and expression data
+colnames(mutation) = paste0(colnames(mutation), "_", "Mut")
+colnames(mutation)[1] = "ModelID"
+colnames(expression) = paste0(colnames(expression), "_", "Exp")
+colnames(expression)[1] = "ModelID"
+
+save(mutation, expression, metadata, file = "CCLE.RData")
+
diff --git a/config_automation.yml b/config_automation.yml
@@ -7,7 +7,7 @@ url-checker: yes
 # Render preview of content with changes (Rmd's and md's are checked)
 render-preview: yes
 # Spell check Rmds and quizzes
-spell-check: yes
+spell-check: no
 # Style any R code
 style-code: yes
 # Test build the docker image if any docker-relevant files have been changed

diff --git a/images/1.png b/images/1.png
diff --git a/images/10.png b/images/10.png
diff --git a/images/2.png b/images/2.png
diff --git a/images/3.png b/images/3.png
diff --git a/images/4.png b/images/4.png
diff --git a/images/5.png b/images/5.png
diff --git a/images/6.png b/images/6.png
diff --git a/images/7.png b/images/7.png
diff --git a/images/8.png b/images/8.png
diff --git a/images/9.png b/images/9.png
diff --git a/images/join.png b/images/join.png
diff --git a/images/kras.png b/images/kras.png
diff --git a/images/lesson3_images.pdf b/images/lesson3_images.pdf
diff --git a/index.Rmd b/index.Rmd
@@ -1,12 +1,12 @@
 ---
-title: "Course Name"
+title: "Season 1 Introduction to R"
 date: "`r format(Sys.time(), '%B, %Y')`"
 site: bookdown::bookdown_site
 documentclass: book
 bibliography: [book.bib]
 biblio-style: apalike
 link-citations: yes
-description: "Description about Course/Book."
+description: ""
 favicon: assets/dasl_favicon.ico
 output:
     bookdown::word_document2:
@@ -15,12 +15,3 @@ output:
 
 # About this Course {-}
 
-
-## Available course formats
-
-This course is available in multiple formats which allows you to take it in the way that best suites your needs. You can take it for certificate which can be for free or fee.
-
-- The material for this course can be viewed without login requirement on this [Bookdown website](LINK HERE). This format might be most appropriate for you if you rely on screen-reader technology.
-- This course can be taken for [free certification through Leanpub](LINK HERE).
-- This course can be taken on [Coursera for certification here](LINK HERE) (but it is not available for free on Coursera).
-- Our courses are open source, you can find the [source material for this course on GitHub](LINK HERE).
-Original file line number
+Diff line change
@@ Expand Up @@
     The course covers fundamentals of R, a high-level programming language, and use it to wrangle data for analysis and visualization. The programming skills you will learn are transferable to learn more about R independently and other high-level languages such as Python. At the end of the class, you will be reproducing analysis from a scientific publication!
-    ```{r}
-    devtools::session_info()
-    ```