Lab 11 - Interactive Visualization
Grab lab file using command line:
# Step 1
cd ~/Documents
mkdir lab11
cd lab11
# Step 2
wget https://raw.githubusercontent.com/USCbiostats/PM566/master/website/content/assignment/11-lab.Rmd
And remember to set eval=TRUE
Learning Goals
- Read in and process the COVID dataset from the New York Times GitHub repository
- Create interactive graphs of different types using
plot_ly()
andggplotly()
functions - Customize the hoverinfo and other plot features
- Create a Choropleth map using
plot_geo()
Lab Description
We will work with COVID data downloaded from the New York Times. The dataset consists of COVID-19 cases and deaths in each US state during the course of the COVID epidemic.
The objective of this lab is to explore relationships between cases, deaths, and population sizes of US states, and plot data to demonstrate this
Steps
I. Reading and processing the New York Times (NYT) state-level COVID-19 data
1. Read in the data
- Read in the COVID data with data.table:fread() from the NYT GitHub repository: “ https://raw.githubusercontent.com/nytimes/covid-19-data/master/us-states.csv"
- Read in the state population data with data.table:fread() from the repository: “ https://raw.githubusercontent.com/COVID19Tracking/associated-data/master/us_census_data/us_census_2018_population_estimates_states.csv""
- Merge datasets
## data extracted from New York Times state-level data from NYT Github repository
# https://github.com/nytimes/covid-19-data
## state-level population information from us_census_data available on GitHub repository:
# https://github.com/COVID19Tracking/associated-data/tree/master/us_census_data
### FINISH THE CODE HERE ###
# load COVID state-level data from NYT
cv_states <- as.data.frame(______________("https://raw.githubusercontent.com/nytimes/covid-19-data/master/us-states.csv"))
### FINISH THE CODE HERE ###
# load state population data
state_pops <- as.data.frame(_____________("https://raw.githubusercontent.com/COVID19Tracking/associated-data/master/us_census_data/us_census_2018_population_estimates_states.csv"))
state_pops$abb <- state_pops$state
state_pops$state <- state_pops$state_name
state_pops$state_name <- NULL
### FINISH THE CODE HERE
cv_states <- merge(cv_states, state_pops, by=________)
2. Look at the data
- Inspect the dimensions,
head
, andtail
of the data - Inspect the structure of each variables. Are they in the correct format?
dim(cv_states)
head(cv_states)
tail(cv_states)
str(cv_states)
3. Format the data
- Make date into a date variable
- Make state into a factor variable
- Order the data first by state, second by date
- Confirm the variables are now correctly formatted
- Inspect the range values for each variable. What is the date range? The range of cases and deaths?
# format the date
cv_states$date <- as.Date(cv_states$date, format="%Y-%m-%d")
# format the state and state abbreviation (abb) variables
state_list <- unique(cv_states$state)
cv_states$state <- factor(cv_states$state, levels = state_list)
abb_list <- unique(cv_states$abb)
cv_states$abb <- factor(cv_states$abb, levels = abb_list)
### FINISH THE CODE HERE
# order the data first by state, second by date
cv_states = cv_states[order(_________, _________),]
# Confirm the variables are now correctly formatted
str(cv_states)
head(cv_states)
tail(cv_states)
# Inspect the range values for each variable. What is the date range? The range of cases and deaths?
head(cv_states)
summary(cv_states)
min(cv_states$date)
max(cv_states$date)
4. Add new_cases
and new_deaths
and correct outliers
-
Add variables for new cases,
new_cases
, and new deaths,new_deaths
:- Hint: You can set
new_cases
equal to the difference between cases on date i and date i-1, starting on date i=2
- Hint: You can set
-
Filter to dates after June 1, 2021
-
Use
plotly
for EDA: See if there are outliers or values that don’t make sense fornew_cases
andnew_deaths
. Which states and which dates have strange values? -
Correct outliers: Set negative values for
new_cases
ornew_deaths
to 0 -
Recalculate
cases
anddeaths
as cumulative sum of updatednew_cases
andnew_deaths
-
Get the rolling average of new cases and new deaths to smooth over time
-
Inspect data again interactively
# Add variables for new_cases and new_deaths:
for (i in 1:length(state_list)) {
cv_subset = subset(cv_states, state == state_list[i])
cv_subset = cv_subset[order(cv_subset$date),]
# add starting level for new cases and deaths
cv_subset$new_cases = cv_subset$cases[1]
cv_subset$new_deaths = cv_subset$deaths[1]
### FINISH THE CODE HERE
for (j in 2:nrow(cv_subset)) {
cv_subset$new_cases[j] = __________ - __________
cv_subset$new_deaths[j] = __________ - __________
}
# include in main dataset
cv_states$new_cases[cv_states$state==state_list[i]] = cv_subset$new_cases
cv_states$new_deaths[cv_states$state==state_list[i]] = cv_subset$new_deaths
}
# Focus on recent dates
cv_states <- cv_states %>% dplyr::filter(date >= "2021-06-01")
### FINISH THE CODE HERE
# Inspect outliers in new_cases using plotly
p1<-ggplot(cv_states, aes(x = date, y = new_cases, color = state)) + ________ + geom_point(size = .5, alpha = 0.5)
ggplotly(p1)
p1<-NULL # to clear from workspace
p2<-ggplot(cv_states, aes(x = date, y = new_deaths, color = state)) + ________ + geom_point(size = .5, alpha = 0.5)
ggplotly(p2)
p2<-NULL # to clear from workspace
# set negative new case or death counts to 0
cv_states$new_cases[cv_states$new_cases<0] = 0
cv_states$new_deaths[cv_states$new_deaths<0] = 0
# Recalculate `cases` and `deaths` as cumulative sum of updated `new_cases` and `new_deaths`
for (i in 1:length(state_list)) {
cv_subset = subset(cv_states, state == state_list[i])
# add starting level for new cases and deaths
cv_subset$cases = cv_subset$cases[1]
cv_subset$deaths = cv_subset$deaths[1]
### FINISH CODE HERE
for (j in 2:nrow(cv_subset)) {
cv_subset$cases[j] = cv_subset$new_cases[j] + cv_subset$_________
cv_subset$deaths[j] = cv_subset$new_deaths[j] + cv_subset$__________
}
# include in main dataset
cv_states$cases[cv_states$state==state_list[i]] = cv_subset$cases
cv_states$deaths[cv_states$state==state_list[i]] = cv_subset$deaths
}
# Smooth new counts
cv_states$new_cases = zoo::rollmean(cv_states$new_cases, k=7, fill=NA, align='right') %>% round(digits = 0)
cv_states$new_deaths = zoo::rollmean(cv_states$new_deaths, k=7, fill=NA, align='right') %>% round(digits = 0)
# Inspect data again interactively
p2<-ggplot(cv_states, aes(x = date, y = new_deaths, color = state)) + geom_line() + geom_point(size = .5, alpha = 0.5)
ggplotly(p2)
#p2=NULL
5. Add additional variables
-
Add population-normalized (by 100,000) variables for each variable type (rounded to 1 decimal place). Make sure the variables you calculate are in the correct format (
numeric
). You can use the following variable names:per100k
= cases per 100,000 populationnewper100k
= new cases per 100,000deathsper100k
= deaths per 100,000newdeathsper100k
= new deaths per 100,000
-
Add a “naive CFR” variable representing
deaths / cases
on each date for each state -
Create a dataframe representing values on the most recent date,
cv_states_today
, as done in lecture
### FINISH CODE HERE
# add population normalized (by 100,000) counts for each variable
cv_states$per100k = as.numeric(format(round(cv_states$cases/(cv_states$________/100000),1),nsmall=1))
cv_states$newper100k = as.numeric(format(round(cv_states$new_cases/(cv_states$________/100000),1),nsmall=1))
cv_states$deathsper100k = as.numeric(format(round(cv_states$deaths/(cv_states$________/100000),1),nsmall=1))
cv_states$newdeathsper100k = as.numeric(format(round(cv_states$new_deaths/(cv_states$________/100000),1),nsmall=1))
# add a naive_CFR variable = deaths / cases
cv_states = cv_states %>% mutate(naive_CFR = round((deaths*100/cases),2))
# create a `cv_states_today` variable
cv_states_today = subset(cv_states, date==max(cv_states$date))
II. Scatterplots
6. Explore scatterplots using plot_ly()
- Create a scatterplot using
plot_ly()
representingpop_density
vs. various variables (e.g.cases
,per100k
,deaths
,deathsper100k
) for each state on most recent date (cv_states_today
)- Color points by state and size points by state population
- Use hover to identify any outliers.
- Remove those outliers and replot.
- Choose one plot. For this plot:
- Add hoverinfo specifying the state name, cases per 100k, and deaths per 100k, similarly to how we did this in the lecture notes
- Add layout information to title the chart and the axes
- Enable
hovermode = "compare"
### FINISH CODE HERE
# pop_density vs. cases
cv_states_today %>%
plot_ly(x = ~pop_density, y = ~cases,
type = _______, mode = 'markers', color = ~______,
size = ~population, sizes = c(5, 70), marker = list(sizemode='diameter', opacity=0.5))
# filter out "District of Columbia"
cv_states_today_filter <- cv_states_today %>% filter(state!="District of Columbia")
# pop_density vs. cases after filtering
cv_states_today_filter %>%
plot_ly(x = ~pop_density, y = ~cases,
type = _______, mode = 'markers', color = ~_______,
size = ~population, sizes = c(5, 70), marker = list(sizemode='diameter', opacity=0.5))
# pop_density vs. deathsper100k
cv_states_today_filter %>%
plot_ly(x = ~pop_density, y = ~deathsper100k,
type = _______, mode = 'markers', color = ~_______,
size = ~population, sizes = c(5, 70), marker = list(sizemode='diameter', opacity=0.5))
# Adding hoverinfo
cv_states_today_filter %>%
plot_ly(x = ~pop_density, y = ~deathsper100k,
type = _______, mode = 'markers', color = ~_______,
size = ~population, sizes = c(5, 70), marker = list(sizemode='diameter', opacity=0.5),
hoverinfo = 'text',
text = ~paste( paste(state, ":", sep=""), paste(" Cases per 100k: ", per100k, sep="") ,
paste(" Deaths per 100k: ", _______, sep=""), sep = "<br>")) %>%
layout(title = "Population-normalized COVID-19 deaths (per 100k) vs. population density for US states",
yaxis = list(title = "Deaths per 100k"), xaxis = list(title = "Population Density"),
hovermode = "compare")
7. Explore scatterplot trend interactively using ggplotly()
and geom_smooth()
- For
pop_density
vs.newdeathsper100k
create a chart with the same variables usinggglot_ly()
- Explore the pattern between
\(x\)
and\(y\)
usinggeom_smooth()
- Explain what you see. Do you think
pop_density
is a correlate ofnewdeathsper100k
?
- Explain what you see. Do you think
### FINISH CODE HERE
p <- ggplot(cv_states_today_scatter, aes(x=pop_density, y=deathsper100k, size=population)) + geom_point() + _______
ggplotly(p)
8. Multiple line chart
- Create a line chart of the
naive_CFR
for all states over time usingplot_ly()
- Use the zoom and pan tools to inspect the
naive_CFR
for the states that had an increase in September. How have they changed over time?
- Use the zoom and pan tools to inspect the
- Create one more line chart, for Florida only, which shows
new_cases
andnew_deaths
together in one plot. Hint: useadd_layer()
- Use hoverinfo to “eyeball” the approximate peak of deaths and peak of cases. What is the time delay between the peak of cases and the peak of deaths?
### FINISH CODE HERE
# Line chart for naive_CFR for all states over time using `plot_ly()`
plot_ly(cv_states, x = ~date, y = ~_______, color = ~state, type = "scatter", mode = "lines")
### FINISH CODE HERE
# Line chart for Florida showing new_cases and new_deaths together
cv_states %>% filter(state=="Florida") %>% plot_ly(x = ~date, y = ~new_cases, type = "scatter", mode = "lines") %>% _______(x = ~date, y = ~new_deaths, type = "scatter", mode = "lines")
9. Heatmaps
Create a heatmap to visualize new_cases
for each state on each date greater than June 1st, 2021
- Start by mapping selected features in the dataframe into a matrix using the tidyr package function
pivot_wider()
, naming the rows and columns, as done in the lecture notes - Use
plot_ly()
to create a heatmap out of this matrix. Which states stand out? - Repeat with
newper100k
variable. Now which states stand out? - Create a second heatmap in which the pattern of
new_cases
for each state over time becomes more clear by filtering to only look at dates every two weeks
### FINISH CODE HERE
# Map state, date, and new_cases to a matrix
library(tidyr)
cv_states_mat <- cv_states %>% select(state, date, new_cases) %>% dplyr::filter(date>as.Date("2021-06-15"))
cv_states_mat2 <- as.data.frame(pivot_wider(cv_states_mat, names_from = state, values_from = ________))
rownames(cv_states_mat2) <- cv_states_mat2$date
cv_states_mat2$date <- NULL
cv_states_mat2 <- as.matrix(cv_states_mat2)
# Create a heatmap using plot_ly()
plot_ly(x=colnames(cv_states_mat2), y=rownames(cv_states_mat2),
z=~cv_states_mat2,
type="heatmap",
showscale=T)
# Repeat with newper100k
cv_states_mat <- cv_states %>% select(state, date, newper100k) %>% dplyr::filter(date>as.Date("2021-06-15"))
cv_states_mat2 <- as.data.frame(pivot_wider(cv_states_mat, names_from = state, values_from = ________))
rownames(cv_states_mat2) <- cv_states_mat2$date
cv_states_mat2$date <- NULL
cv_states_mat2 <- as.matrix(cv_states_mat2)
plot_ly(x=colnames(cv_states_mat2), y=rownames(cv_states_mat2),
z=~cv_states_mat2,
type="heatmap",
showscale=T)
# Create a second heatmap after filtering to only include dates every other week
filter_dates <- seq(as.Date("2021-06-15"), as.Date("2021-11-01"), by=________)
cv_states_mat <- cv_states %>% select(state, date, newper100k) %>% filter(date %in% filter_dates)
cv_states_mat2 <- as.data.frame(pivot_wider(cv_states_mat, names_from = state, values_from = ________))
rownames(cv_states_mat2) <- cv_states_mat2$date
cv_states_mat2$date <- NULL
cv_states_mat2 <- as.matrix(cv_states_mat2)
# Create a heatmap using plot_ly()
plot_ly(x=colnames(cv_states_mat2), y=rownames(cv_states_mat2),
z=~cv_states_mat2,
type="heatmap",
showscale=T)
10. Map
- Create a map to visualize the
naive_CFR
by state on October 15, 2021 - Compare with a map visualizing the
naive_CFR
by state on most recent date - Plot the two maps together using
subplot()
. Make sure the shading is for the same range of values (google is your friend for this) - Describe the difference in the pattern of the CFR.
### For specified date
pick.date = "2021-10-15"
# Extract the data for each state by its abbreviation
cv_per100 <- cv_states %>% filter(date==pick.date) %>% select(state, abb, newper100k, cases, deaths) # select data
cv_per100$state_name <- cv_per100$state
cv_per100$state <- cv_per100$abb
cv_per100$abb <- NULL
# Create hover text
cv_per100$hover <- with(cv_per100, paste(state_name, '<br>', "Cases per 100k: ", newper100k, '<br>', "Cases: ", cases, '<br>', "Deaths: ", deaths))
# Set up mapping details
set_map_details <- list(
scope = 'usa',
projection = list(type = 'albers usa'),
showlakes = TRUE,
lakecolor = toRGB('white')
)
# Make sure both maps are on the same color scale
shadeLimit <- 125
# Create the map
fig <- plot_geo(cv_per100, locationmode = 'USA-states') %>%
add_trace(
z = ~newper100k, text = ~hover, locations = ~state,
color = ~newper100k, colors = 'Purples'
)
fig <- fig %>% colorbar(title = paste0("Cases per 100k: ", pick.date), limits = c(0,shadeLimit))
fig <- fig %>% layout(
title = paste('Cases per 100k by State as of ', pick.date, '<br>(Hover for value)'),
geo = set_map_details
)
fig_pick.date <- fig
#############
### Map for today's date
# Extract the data for each state by its abbreviation
cv_per100 <- cv_states_today %>% select(state, abb, newper100k, cases, deaths) # select data
cv_per100$state_name <- cv_per100$state
cv_per100$state <- cv_per100$abb
cv_per100$abb <- NULL
# Create hover text
cv_per100$hover <- with(cv_per100, paste(state_name, '<br>', "Cases per 100k: ", newper100k, '<br>', "Cases: ", cases, '<br>', "Deaths: ", deaths))
# Set up mapping details
set_map_details <- list(
scope = 'usa',
projection = list(type = 'albers usa'),
showlakes = TRUE,
lakecolor = toRGB('white')
)
# Create the map
fig <- plot_geo(cv_per100, locationmode = 'USA-states') %>%
add_trace(
z = ~newper100k, text = ~hover, locations = ~state,
color = ~newper100k, colors = 'Purples'
)
fig <- fig %>% colorbar(title = paste0("Cases per 100k: ", Sys.Date()), limits = c(0,shadeLimit))
fig <- fig %>% layout(
title = paste('Cases per 100k by State as of', Sys.Date(), '<br>(Hover for value)'),
geo = set_map_details
)
fig_Today <- fig
### Plot together
________(fig_pick.date, fig_Today, nrows = 2, margin = .05)