fhdsl · kweav · Jul 23, 2024 · Jul 23, 2024 · Aug 2, 2024 · Nov 6, 2024
diff --git a/01-intro.Rmd b/01-intro.Rmd
@@ -5,18 +5,24 @@ ottrpal::set_knitr_image_path()
 
 # Introduction
 
+This course is meant as a follow up to the ITCR course "Considerations for Bioinformatic Data Visualization", employing best practices while constructing data visualizations (both guided and a self-guided project) and interpreting the conclusions presented in the visualizations.
 
-## Motivation
+## Target Audience  
 
+The course is intended for cancer researchers with experience using basic informatics tools and who have an interest in data visualization.
 
-## Target Audience  
+## Motivation
 
-The course is intended for ...
+Due to the frequent use of automated algorithms to collect and process data as well as the large size of datasets, it is critical to look at collected data and produce effective summaries. Data visualization is useful for exploration, validation, and presentation of research, aiding in the understanding of underlying biology in data sets, debugging errors in informatics workflows, and identifying/avoiding sources of bias. This course is designed to guide learners through constructing effective and accessible visualizations and point to additional practice and documentation resources.
 
 ## Curriculum  
 
-The course covers...
+The course covers using data visualization tools to construct effective and accessible data visualizations.  
+
 
+```{r out.width = "100%", echo = FALSE}
+ottrpal::include_slide("https://docs.google.com/presentation/d/1cbxc79tKxbH7PZJC18IQcfOfZALNwwVs7WtiiPxD6gU/edit#slide=id.g3015fd53a67_0_22")
+```
 
 ```{r}
 devtools::session_info()

diff --git a/02_cancer_informatic_data_viz.Rmd b/02_cancer_informatic_data_viz.Rmd
@@ -0,0 +1,17 @@
+# Data Visualization for Cancer Informatics
+
+```{r, include = FALSE}
+ottrpal::set_knitr_image_path()
+```
+
+## Learning Objectives
+
+This chapter will cover:
+
+- {LO1}
+- {LO2}
+
+## Common types of Cancer Data
+## Common research questions when working with cancer data
+## Most common graph types in cancer informatics
+## Available technologies for data visualizations in cancer informatics
diff --git a/03_practice_overview.Rmd b/03_practice_overview.Rmd
@@ -0,0 +1,12 @@
+# Practicing Cancer Informatics Data Visualizations
+
+```{r, include = FALSE}
+ottrpal::set_knitr_image_path()
+```
+
+## Learning Objectives
+
+This chapter will cover:
+
+- {LO1}
+- {LO2}
diff --git a/03a_practice_general.Rmd b/03a_practice_general.Rmd
@@ -0,0 +1,12 @@
+# Practicing: With General Data
+
+```{r, include = FALSE}
+ottrpal::set_knitr_image_path()
+```
+
+## Learning Objectives
+
+This chapter will cover:
+
+- {LO1}
+- {LO2}
diff --git a/03b_practice_singlecell.Rmd b/03b_practice_singlecell.Rmd
@@ -0,0 +1,12 @@
+# Practicing: With Single Cell Data
+
+```{r, include = FALSE}
+ottrpal::set_knitr_image_path()
+```
+
+## Learning Objectives
+
+This chapter will cover:
+
+- {LO1}
+- {LO2}
diff --git a/04_other_practice.Rmd b/04_other_practice.Rmd
@@ -0,0 +1,17 @@
+# Other ways to practice
+
+```{r, include = FALSE}
+ottrpal::set_knitr_image_path()
+```
+
+## Learning Objectives
+
+This chapter will cover:
+
+- {LO1}
+- {LO2}
+
+
+## Bioviz data visualization challenges
+## Plotnine Contest Gallery
+## Case studies from the Fred Hutch Data Visualization Center
diff --git a/05_wrapping_up.Rmd b/05_wrapping_up.Rmd
@@ -0,0 +1,18 @@
+# Wrapping up
+
+```{r, include = FALSE}
+ottrpal::set_knitr_image_path()
+```
+
+## Learning Objectives
+
+This chapter will cover:
+
+- {LO1}
+- {LO2}
+
+## In summary
+
+## Additional Resources
+
+## See next 
diff --git a/README.md b/README.md
@@ -1,14 +1,14 @@
-# {Course Name}
+# Cancer Informatics Data Visualization in Practice
 
 This course was created from [this GitHub template](https://github.com/jhudsl/OTTR_Template).
 
-You can see the rendered course material here: {Link to rendered bookdown and/or to the Leanpub.}
+You can see the rendered course material here: https://hutchdatascience.org/DataViz_Practice/
 
 If you would like to contribute to this course material, take a look at the [OTTR documentation](https://www.ottrproject.org/).
 
 ## About this course
 
-This course introduces {info on what this course introduces}
+This ITN course focuses on practicing best practices in data visualization by discussing common graph types used within Cancer Informatics, building graphs (while employing best practices), showcasing ITCR tools that are helpful for data visualization of cancer research data, and providing additional resources for further visualization practice.
 
 ## Learning Objectives
 

diff --git a/_bookdown.yml b/_bookdown.yml
@@ -1,9 +1,14 @@
-book_filename: "Course_Name"
+book_filename: "Cancer Informatics Data Visualization in Practice"
 chapter_name: "Chapter "
-repo: https://github.com/jhudsl/OTTR_Template/
+repo: https://github.com/fhdsl/DataViz_Practice/
 rmd_files: ["index.Rmd",
             "01-intro.Rmd",
-            "02-chapter_of_course.Rmd",
+            "02_cancer_informatic_data_viz.Rmd",
+            "03_practice_overview.Rmd",
+            "03a_practice_general.Rmd",
+            "03b_practice_singlecell.Rmd",
+            "04_other_practice.Rmd",
+            "05_wrapping_up.Rmd",
             "About.Rmd",
             "References.Rmd"]
 new_session: yes

diff --git a/_output.yml b/_output.yml
@@ -1,16 +1,18 @@
 bookdown::gitbook:
-  css: assets/style.css
+  css: assets/style_ITN.css
   includes:
-    before_body: assets/big-image.html
-    after_body: [assets/footer.html, assets/open-new-tab.html]
-    highlight: tango
+    before_body: assets/big-image-itcr.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://www.itcrtraining.org/"><img src="assets/ITN_logo.png" style="padding-left: 15px; padding-top: 8px;"</a>
       after: |
        <p style="text-align:center;"> <a href="https://www.ottrproject.org/" target="blank" > This content was published with</a> <a href="https://bookdown.org/" target="blank"> bookdown using</a> </p>
        <p style="text-align:center;"> <a href="https://github.com/jhudsl/OTTR_Template"> The OTTR Template by:</a></p>
        <p style="text-align:center;"> <a href="http://jhudatascience.org/"> The Johns Hopkins Data Science Lab </a></p>
+       <a href="http://jhudatascience.org/"><img src="https://jhudatascience.org/images/dasl.png" style=" width: 80%; filter: grayscale(100%); padding-left: 40px; padding-top: 8px; vertical-align: top "</a>
        <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/hc8Xt3Y2Znjb6M4Y7"> Click here to provide feedback</a> <img src="assets/itcr_arrow.png" style=" width: 10%" ></span></div></p>
diff --git a/assets/ITN_favicon.ico b/assets/ITN_favicon.ico
diff --git a/assets/ITN_logo.png b/assets/ITN_logo.png
diff --git a/assets/big-image-itcr.html b/assets/big-image-itcr.html
@@ -0,0 +1,12 @@
+<head>
+  <meta name="viewport" content="width=device-width,minimum-scale=1.0,maximum-scale=1.0,initial-scale=1.0">
+  <!--script src="https://kit.fontawesome.com/6a26f47516.js"></script-->
+  <!--<script src="assets/hideOutput.js"></script>-->
+  <link href="assets/style_ITN.css" rel="stylesheet">
+</head>
+
+
+
+<div class="hero-image-container"> 
+  <img class= "hero-image" src="assets/itcr_main_image.png">
+</div>
diff --git a/assets/itcr_main_image.png b/assets/itcr_main_image.png