The lollipop charts are used to show variation of a variable with time (most commonly). In this example I am using the weekly number of leishmaniasis patients in each district of Sri Lanka from Jan 2014 - Dec 2015.

Loading packages (pacman install and load all the packages)

ggplot2 - for charts gganimate - to animate the charts rio - to import data dplyr & tidyr - to arrange and tidy the data gifski - To render the animation

pacman::p_load(ggplot2, gganimate, rio, tidyr, dplyr, gifski)

#pacman (package manager install and load all the packages.)

Importing data and checking

clTemp <- import("C:/Users/hp/Documents/MEGAsync/TWData/cltdata.csv")
cltraw <- clTemp[1:103] # selecting the exact range of data from the imported data sheets. 

head(cltraw)[1:4] # Checking first four columns of the data frame
##       District 3/1/2014 10/1/2014 17/01/2014
## 1      Colombo        0         0          0
## 2      Gampaha        1         0          0
## 3     Kalutara        0         0          0
## 4        Kandy        0         0          0
## 5       Matale        0         0          0
## 6 Nuwara Eliya        0         0          0

In the data frame, a week is a column. But we need to get all the weeks as a row of a new column called week. This is done by pivot_longer function (gather() is another possible function for this. But that has been stopped developing and may not be available in coming versions. So I am using pivot function)

Lets pivot

cltpiv <- pivot_longer(cltraw, cols = 2:103) 


cltpiv %>% tail(10)
## # A tibble: 10 x 3
##    District name       value
##    <chr>    <chr>      <int>
##  1 Kalmune  23/10/2015    NA
##  2 Kalmune  30/10/2015    NA
##  3 Kalmune  6/11/2015     NA
##  4 Kalmune  13/11/2015    NA
##  5 Kalmune  20/11/2015    NA
##  6 Kalmune  27/11/2015    NA
##  7 Kalmune  4/12/2015     NA
##  8 Kalmune  11/12/2015    NA
##  9 Kalmune  18/12/2015    NA
## 10 Kalmune  25/12/2015    NA
# I've included data for all 26 districts. So for 26*101 should be the num of rows in cltar

nrow(cltpiv)
## [1] 2652

Pivoting converts the variable into characters. So I will create a Week clumn separately and cbind it to the data frame.

startDate <- as.Date("2014-01-03")

Weekraw <- seq(startDate, by="1 week", length.out=102) 

Week <- rep(Weekraw, times = 26) # coz in the long format need one repitition for each district

tail(Week) # To check if the data is fitting
## [1] "2015-11-06" "2015-11-13" "2015-11-20" "2015-11-27" "2015-12-04"
## [6] "2015-12-11"
#Lets combine Week to cltar

clt_bound <- cbind(cltpiv, Week)

cltar <- clt_bound %>% select(-name) #remove unnecessary column

In this data set missing values means the number of patients = 0

Lets convert all the “na” s to 0

cltar[is.na(cltar)] <- 0

head(cltar)
##   District value       Week
## 1  Colombo     0 2014-01-03
## 2  Colombo     0 2014-01-10
## 3  Colombo     0 2014-01-17
## 4  Colombo     0 2014-01-24
## 5  Colombo     0 2014-01-31
## 6  Colombo     0 2014-02-07
clt <- cltar # for the ease of calling

colnames(clt) <- c("District", "Patients", "Week") # Renaming columns

Creating the basic plot

p <- ggplot(clt,
       aes(x=District, y=Patients, label = District, color = District)) + 
  geom_point(stat = "identity", size = 4) + 
  geom_segment(aes(
    y = 26,
    x = District,
    yend = Patients,
    xend = District)
    )

Shifting axis and adding text to bars

p <- ggplot(clt,
       aes(x=District, y=Patients, label = District, color = District)) + 
  geom_point(stat = "identity", size = 4) + 
  geom_segment(aes(
    y = 26,
    x = District,
    yend = Patients,
    xend = District)
    ) + 
  geom_text(color = "block", size = 4) + #adding text to bar
  coord_flip() # shifting axis

Making the animation

p <- ggplot(clt,
       aes(x=District, y=Patients, label = District, color = District)) + 
  geom_point(stat = "identity", size = 4) + 
  geom_segment(aes(
    y = 26,
    x = District,
    yend = Patients,
    xend = District)
    ) + 
  geom_text(color = "block", size = 4) + #adding text to bar
  coord_flip() + # shifting axis
  theme(legend.position = "none") + #removing legend
    labs (title = "Week: {frame_time}", x= "Week", y = "Patients") + # The animation codes starts here
    transition_time(Week)
  ease_aes('linear')
## <ggproto object: Class EaseAes, gg>
##     aes_names: 
##     aesthetics: 
##     default: linear
##     get_ease: function
##     super:  <ggproto object: Class EaseAes, gg>
animate(p, duration = 40, fps = 20, width = 500, height = 500, renderer = gifski_renderer())

# anim_save("output.gif")

You can change duration and the size of the animation. by changing the “animate” function

Please note that you could use anim_save(“output.gif”) to save the animation as a GIF file. I have removed it as it brings an error when knitting the markdown file.