bhamidipati_bioinformatics_v4.Rmd

---
title: "bhamidipati_bioinformatics"
author: 'Sai Krishna Bhamidipati (PID: A59010579)'
date: "`r Sys.Date()`"
output: github_document
---

**Sai Krishna Bhamidipati**
**PID: A59010579**

```{r message=FALSE, warning=FALSE, paged.print=FALSE}

#Loading all necessary functions

library(tidyverse)
library(lubridate)
library("ggplot2")
library(dplyr)
```


```{r message=FALSE, warning=FALSE, paged.print=FALSE}

#Reading the COVID-19 Variant Data from the CHHS website

data <- read.csv("covid19_variants.csv")

#Just making sure to parse out the dates into year-month-day formats
data$date <- ymd(data$date)
```


```{r message=FALSE, warning=FALSE, paged.print=FALSE}

#Removing rows containing "Total"s.
data_1 <- data[- grep("Total", data$variant_name),]

#Removing rows containing "Other" as per the example graph given.
data_2 <- data_1[- grep("Other", data_1$variant_name),]

#Removing June 2022 stuff, since it was not there in the example given.
data_3 <- data_2[- grep("2022-06", data_2$date),]
```


```{r message=FALSE, warning=FALSE, paged.print=FALSE}

#package that has theme components for ggplot2.
library(hrbrthemes)

#plotting the data with date on x axis and percentage of sequenced specimens on y axis
  ggplot( data = data_3, mapping = aes( x=date, y=percentage, color=variant_name ) )+
  
#Grouping according to variant types
  geom_line(aes( group=variant_name ))+
  
#Adding title for the graph and label for y-axis.
  labs(title = "Covid-19 Variants in California", x=" ",y = "Percentage of sequenced specimens", caption = "Data source: <https://www.cdph.ca.gov>")+
  
#Scaling the x-axis to show 1 month intervals, and the labels having abbreviated months 
#and unabbreviated year. Also, as per the example given, only including data until May 2022
  scale_x_date(date_breaks = "1 month", date_labels = "%b %Y", limit=c(as.Date("2021-01-01"),as.Date("2022-05-1")))+
  
#Rotating the dates to an angle
  theme_ipsum() +
  theme(axis.text.x=element_text(angle=60, hjust=1))+
  
#Removing x-axis and legend titles to match the example given.
  theme(axis.title.x = element_blank(),legend.title=element_blank())+
  
#Adding a border for the graph, as in the example.
  theme(panel.border = element_rect(color = "black",
                                    fill = NA,
                                    size = 0.5))+
#Centering the y-axis title
  theme(axis.title.y = element_text(hjust=0.5))
```