checking_data_validity.Rmd

---
title: "Untitled"
output: html_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```


Checking that the metadata and genome names line up

```{r}
library(tidyverse)
metadata <- read_csv('data/curry_county_population_data_site_host_nextstrain.csv')
seqs <- metacoder::read_fasta('data/curryco_mt.fasta')

all(names(seqs) %in% metadata$strain)
all(metadata$strain %in% names(seqs))
```

seems to be fine


## Figure out how to group samples geographically

```{r}
library(tidyverse)
library(ggplot2)
metadata <- read_csv('data/curry_county_population_data_site_host_nextstrain.csv')
```

plot sites to see if sites would be a good grouping

```{r}
metadata %>%
  mutate(site = factor(site)) %>%
  ggplot() +
  geom_point(aes(x = lon, y = lat, color = site))
```