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Changed book style and started adding shell per outline #6

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20 changes: 20 additions & 0 deletions 02_what_why_intro.Rmd
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# What is Data Visualization?

```{r, include = FALSE}
ottrpal::set_knitr_image_path()
```

## Learning Objectives

This chapter will cover:

- {LO1}
- {LO2}

## What is Data Visualization?

### Exploratory Data Analysis (EDA)
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I do like the exploratory vs explanatory dichotomy for explaining the aims of visualization: https://laderast.github.io/data_storytelling_bdc/#5


### Polished Visualizations for sharing

## Why is data visualization so important?
30 changes: 30 additions & 0 deletions 03_background_data_graph_info.Rmd
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# Which visualization should I use?

A data visualization is made up of data and ...

Deciding which data visualization to use ...

```{r, include = FALSE}
ottrpal::set_knitr_image_path()
```

## Learning Objectives

This chapter will cover:

- {LO1}
- {LO2}

## Data types

## Graph types
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Per @carriewright11 's suggestion, I like showing a decision tree like this to help people decide on visualizations: https://www.data-to-viz.com/

Probably need to also expand to include cancer informatics-specific visualizations, including genomics/volcano plots, etc


## Data encodings

### Shape

### Color

### Area, Line, point, ...

### Labels
28 changes: 28 additions & 0 deletions 04_how_to_improve_viz.Rmd
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# High quality and inclusive data visualizations

```{r, include = FALSE}
ottrpal::set_knitr_image_path()
```

## Learning Objectives

This chapter will cover:

- {LO1}
- {LO2}

## Visual Design Principles
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Can be helpful to talk about preattentive attributes and how they're used in viz design: https://laderast.github.io/data_storytelling_bdc/#22


## Accessibility Considerations

### Color palettes

### Labels

### Captions and alternative text descriptions

## Ethical Considerations

### Data Distortions

## Annotations and other points of reference
18 changes: 18 additions & 0 deletions 05_wrapping_up.Rmd
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# Wrapping up

```{r, include = FALSE}
ottrpal::set_knitr_image_path()
```

## Learning Objectives

This chapter will cover:

- {LO1}
- {LO2}

## In summary

## Additional Considerations

## See next
6 changes: 3 additions & 3 deletions README.md
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# {Course Name}
# Considerations for Bioinformatic Data Visualization

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_Considerations/

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 introduces considerations for best practices in data visualization focusing on and discussing topics such as defining what data visualization is, utilizing exploratory data analysis, employing visual design principles, and making visualizations accessible.

## Learning Objectives

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9 changes: 6 additions & 3 deletions _bookdown.yml
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book_filename: "Course_Name"
book_filename: "Considerations for Bioinformatic Data Visualization"
chapter_name: "Chapter "
repo: https://github.com/jhudsl/OTTR_Template/
repo: https://github.com/fhdsl/DataViz_Considerations/
rmd_files: ["index.Rmd",
"01-intro.Rmd",
"02-chapter_of_course.Rmd",
"02_what_why_intro.Rmd",
"03_background_data_graph_info.Rmd",
"04_how_to_improve_viz.Rmd",
"05_wrapping_up.Rmd",
"About.Rmd",
"References.Rmd"]
new_session: yes
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12 changes: 7 additions & 5 deletions _output.yml
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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>
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12 changes: 12 additions & 0 deletions assets/big-image-itcr.html
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<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>
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