<commit_before>---
feature_text: |
  ## Genomic Visualization and Interpretations
title: Q & A, Discussion, Integrated Assignments, and Working with Your Own Data
categories:
    - Module 6
feature_image: "assets/genvis-dna-bg_optimized_v1a.png"
date: 0006-01-01
---

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### Additional resources
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Cum quem justo urbanitas no, mei inermis alienum indoctum ei. Cu assum ludus soluta per. Sea at idque perpetua, ex fabulas hendrerit adversarium per, sit impedit recteque necessitatibus an. Quo fabulas feugait scriptorem et.

### Additional Exercises
Lorem ipsum dolor sit amet, munere intellegat cu mel. Ea sint summo exerci mei. Autem tritani scaevola mei ea, sonet oporteat vel cu. Duo cu erat libris vulputate. Cum possim copiosae facilisi ea, partiendo tincidunt voluptatibus ne est, vix ea justo animal.

Cum quem justo urbanitas no, mei inermis alienum indoctum ei. Cu assum ludus soluta per. Sea at idque perpetua, ex fabulas hendrerit adversarium per, sit impedit recteque necessitatibus an. Quo fabulas feugait scriptorem et.

[Module 6 Lecuture](http://genviz.org/lectures/GenViz_Module6_Lecture.pptx)<commit_msg>added initial exercise<commit_after>---
feature_text: |
  ## Genomic Visualization and Interpretations
title: Q & A, Discussion, Integrated Assignments, and Working with Your Own Data
categories:
    - Module 6
feature_image: "assets/genvis-dna-bg_optimized_v1a.png"
date: 0006-01-01
---

Lorem ipsum dolor sit amet, munere intellegat cu mel. Ea sint summo exerci mei. Autem tritani scaevola mei ea, sonet oporteat vel cu. Duo cu erat libris vulputate. Cum possim copiosae facilisi ea, partiendo tincidunt voluptatibus ne est, vix ea justo animal.


#### Additional Exercises
In 1854 there was cholera epedemic in the Soho district of London kown as the [Golden square outbreak](https://en.wikipedia.org/wiki/1854_Broad_Street_cholera_outbreak). Ultimately a particularly virulent strain of the disease caused the deaths of 616 individuals. At this time there were two competing theories as to the cause of the outbreak. The commonly held miasma theory postulated that foul air from decaying organic matter was the cause of the disease. A physician by the name of [John Snow](https://en.wikipedia.org/wiki/John_Snow) had published years early germ theory, specifically that cholera was caused by an unkown germs presence in contaminated water. The [Golden square outbreak](https://en.wikipedia.org/wiki/1854_Broad_Street_cholera_outbreak) allowed [John Snow](https://en.wikipedia.org/wiki/John_Snow) with the help of [Henry Whitehead](https://en.wikipedia.org/wiki/Henry_Whitehead_(priest)) to map the deaths of the outbreak in relation to public water pumps around the area. Eventually this work led to the debunking of miasma theory. In this exercise try and recreate the famous map originally created by [<NAME>](https://en.wikipedia.org/wiki/John_Snow) to support his theory, and example of which is shown below. You'll need to install the package [cholera](https://cran.r-project.org/web/packages/cholera/index.html) and use the data frames specified below.

* *topics covered:* ggplot2, basic R
* *difficulty:* 2/5

```R
install.packages(cholera)
data(roads)
data(pumps)
data(fatalities.address)
data()
```

[Module 6 Lecuture](http://genviz.org/lectures/GenViz_Module6_Lecture.pptx)
{'fraction_non_alphanumeric': 0.06978567694720335, 'fraction_numerical': 0.01097752221641401, 'mean_word_length': 4.924148606811145, 'pattern_counts': {'":': 0, '<': 4, '<?xml version=': 0, '>': 4, 'https://': 7, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 4, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '1752121', 'n_tokens_mistral': 1294, 'n_tokens_neox': 1200, 'n_words': 482}