06 AE Attendances ggplot2 plot.R

# 06 AE Attendances ggplot2 plot.R

# We start by Loading previous data set.
# AEATT_plot 
names(AEATT_plot)
head(AEATT_plot)
# 6.1. Plot 01: A&E Attendances: Type 1 Departments - Major A&E
# Data: AEATT_plot
# Variables: period,type_1_Major_att
#type_1_Major_att = type_1_departments_major_a_e,
# type_2_Single_esp_att = type_2_departments_single_specialty,
# type_3_other_att = type_3_departments_other_a_e_minor_injury_unit,
# total_att = total_attendances

# Features added to initial ggplot() object
# 1. Create initial ggplot() object
# 2. Add color to line  
# 3. Add new geom to plot using geom_point()  
# 4. Modify X and Y axis labels
# 5. Remove tick marks 
# 6. Include theme 
#     Arrange all themes into a single output image using grid-arrange()
# 7. Modify continuous Y axis
# 8. Add a smooth line to the line chart


# 1. Initial plot using Type I attendances data across time
library(tidyverse)
library(gridExtra)

head(AEATT_plot)
names(AEATT_plot)

#[1] "period"                "type_1_Major_att"      "type_2_Single_esp_att"
#[4] "type_3_other_att"      "total_att" 


# We include geom_line() to display an initial plot
# geom_line()

TypeI_att_plot <- AEATT_plot %>% 
                  select(period, type_1_Major_att) %>% 
                  ggplot(aes(x = period, y = type_1_Major_att )) +
                  geom_line() +
                  labs(title = "A&E Attendances in England: Type 1 Departments - Major A&E",
                       subtitle ="Source: https://www.england.nhs.uk/statistics/statistical-work-areas/ae-waiting-times-and-activity/")

TypeI_att_plot


# 2. Add color to line  
# Interesting resource from nhs-R-community GitHub repo with 
# NHSR Color Themes

# https://github.com/nhs-r-community/NHSRtheme
# https://nhsengland.github.io/nhs-r-reporting/documentation/nhs-colours.html

# We include new parameters in geom_line() geom 
# geom_line()
# 1. Include colour geom_line(color = "#0072CE")
# 2. Include line size (1)
# 3. Include linetype (linetype="dashed", linetype="dotted", 0  is for “blank”, 1 is for “solid”, 2 is for “dashed”)
# NHS Blue	#005EB8
# NHS Bright Blue	#0072CE 
TypeI_att_plot <- AEATT_plot %>% 
                      select(period, type_1_Major_att) %>% 
                      ggplot(aes(x = period, y = type_1_Major_att)) +
                      geom_line(color="#0072CE", size=1,  linetype=1) +
                      labs(title = "A&E Attendances in England: Type 1 Departments - Major A&E",
                      subtitle ="Source: https://www.england.nhs.uk/statistics/statistical-work-areas/ae-waiting-times-and-activity/")

TypeI_att_plot

# Save plot
ggsave("plots/01_A&E_Attendances_Type_1_England.png", width = 6, height = 4)

# 3. Add new geom to plot geom_point()  
# geom_point()
#   Parameters:  
#       show.legend: logical. Should this layer be included in the legends? NA, the default, includes if any aesthetics are mapped. FALSE never includes,

# Source or NHS England colors
# https://www.england.nhs.uk/nhsidentity/identity-guidelines/colours/

# I include this time two hues of NHS blues in the plot
# NHS Bright Blue #0072CE ff
# NHS Aqua Blue #00A9CE

TypeI_dot_line_plot <- AEATT_plot %>% 
                  select(period, type_1_Major_att) %>% 
                  ggplot(aes(x = period, y = type_1_Major_att)) +
                  geom_line(color="#0072CE", size=1,  linetype=1) +
                  # Included new geom
                  geom_point(fill="#00A9CE",shape=21,show.legend = FALSE) +
                  labs(title = "A&E Attendances in England: Type 1 Departments - Major A&E",
                       subtitle ="Source: https://www.england.nhs.uk/statistics/statistical-work-areas/ae-waiting-times-and-activity/")

TypeI_dot_line_plot

ggsave("plots/02_A&E_Attendances_Type_1_England_line_point_geom.png", width = 6, height = 4)

# 4. Modify X and Y axis labels
Axis_labels_plot <- AEATT_plot %>% 
                          select(period, type_1_Major_att) %>% 
                          ggplot(aes(x = period, y = type_1_Major_att)) +
                          geom_line(color="#0072CE", size=1,  linetype=1) +
                          # Included new geom
                          geom_point(fill="#00A9CE",shape=21,show.legend = FALSE) +
                          labs(title = "A&E Attendances in England: Type 1 Departments - Major A&E",
                               subtitle ="Source: https://www.england.nhs.uk/statistics/statistical-work-areas/ae-waiting-times-and-activity/",
                               # Change X and Y axis labels
                               x = "Period", 
                               y = "Type I Attendances") 
                          
Axis_labels_plot

ggsave("plots/03_A&E_Attendances_Type_1_England_aixs_titles.png", width = 6, height = 4)

# 5. Remove tick marks 
# theme(axis.ticks = element_blank())

Axis_ticks_removed <- AEATT_plot %>% 
  select(period, type_1_Major_att) %>% 
  ggplot(aes(x = period, y = type_1_Major_att)) +
  geom_line(color="#0072CE", size=1,  linetype=1) +
  # Included new geom
  geom_point(fill="#00A9CE",shape=21,show.legend = FALSE) +
  labs(title = "A&E Attendances in England: Type 1 Departments - Major A&E",
       subtitle ="Source: https://www.england.nhs.uk/statistics/statistical-work-areas/ae-waiting-times-and-activity/",
       # Change X and Y axis labels
       x = "Period", 
       y = "Type I Attendances") +
  theme (axis.ticks = element_blank())

Axis_ticks_removed

ggsave("plots/04_A&E_Attendances_Type_1_England_Axis_ticks_removed.png", width = 6, height = 4)

# 6. Include theme 
# Arrange different plots using gridExtra


# Theme bw
# theme_bw()
TypeI_theme_bw  <- AEATT_plot %>% 
                      select(period, type_1_Major_att) %>% 
                      ggplot(aes(x = period, y = type_1_Major_att)) +
                      geom_line(color="#0072CE", size=1,  linetype=1) +
                      # Included new geom
                      geom_point(fill="#00A9CE",shape=21,show.legend = FALSE) +
                      labs(title = "A&E Attendances \n Theme_bw",
                           subtitle ="Source: https://www.england.nhs.uk/statistics/statistical-work-areas/ae-waiting-times-and-activity/",
                           # Change X and Y axis labels
                           x = "Period", 
                           y = "Type I Attendances") +
                      theme (axis.ticks = element_blank()) +
                      theme_bw()

TypeI_theme_bw

# Theme light
# theme_light()

TypeI_theme_light  <- AEATT_plot %>% 
  select(period, type_1_Major_att) %>% 
  ggplot(aes(x = period, y = type_1_Major_att)) +
  geom_line(color="#0072CE", size=1,  linetype=1) +
  # Included new geom
  geom_point(fill="#00A9CE",shape=21,show.legend = FALSE) +
  labs(title = "A&E Attendances \n Theme_light",
       subtitle ="Source: https://www.england.nhs.uk/statistics/statistical-work-areas/ae-waiting-times-and-activity/",
       # Change X and Y axis labels
       x = "Period", 
       y = "Type I Attendances") +
  theme (axis.ticks = element_blank()) +
  theme_light()

TypeI_theme_light

# Theme classic
# theme_classic()

TypeI_theme_classic  <- AEATT_plot %>% 
  select(period, type_1_Major_att) %>% 
  ggplot(aes(x = period, y = type_1_Major_att)) +
  geom_line(color="#0072CE", size=1,  linetype=1) +
  # Included new geom
  geom_point(fill="#00A9CE",shape=21,show.legend = FALSE) +
  labs(title = "A&E Attendances \n Theme_classic",
       subtitle ="Source: https://www.england.nhs.uk/statistics/statistical-work-areas/ae-waiting-times-and-activity/",
       # Change X and Y axis labels
       x = "Period", 
       y = "Type I Attendances") +
  theme (axis.ticks = element_blank()) +
  theme_classic()

TypeI_theme_classic

# Theme dark (last of base themes)
# theme_dark() 

TypeI_theme_dark  <- AEATT_plot %>% 
  select(period, type_1_Major_att) %>% 
  ggplot(aes(x = period, y = type_1_Major_att)) +
  geom_line(color="#0072CE", size=1,  linetype=1) +
  # Included new geom
  geom_point(fill="#00A9CE",shape=21,show.legend = FALSE) +
  labs(title = "A&E Attendances, \n Theme_dark",
       subtitle ="Source: https://www.england.nhs.uk/statistics/statistical-work-areas/ae-waiting-times-and-activity/",
       # Change X and Y axis labels
       x = "Period", 
       y = "Type I Attendances") +
  theme (axis.ticks = element_blank()) +
  theme_dark()

TypeI_theme_dark

# Arrange all plots into a single image using grid-arrange()
GRID_PLOT <- grid.arrange(TypeI_theme_bw,TypeI_theme_light,
             TypeI_theme_classic,TypeI_theme_dark,
             ncol=4)

ggsave("plots/05_A&E_Attendances_Grid_Arrange_themes_gallery_02.png", width = 6, height = 4)

# 7. Modify continuous Y axis

MIN_att_value <- min(AEATT_plot$type_1_Major_att)
MIN_att_value
# [1] 1053707
MAX_att_value <- max(AEATT_plot$type_1_Major_att)
MAX_att_value
# [1] 1373061

TypeI_cont_y_axis  <- AEATT_plot %>% 
                          select(period, type_1_Major_att) %>% 
                          ggplot(aes(x = period, y = type_1_Major_att)) +
                          geom_line(color="#0072CE", size=1,  linetype=1) +
                          # Included new geom
                          geom_point(fill="#00A9CE",shape=21,show.legend = FALSE) +
                          labs(title = "A&E Attendances in England: Type 1 Departments - Major A&E",
                               subtitle ="Source: https://www.england.nhs.uk/statistics/statistical-work-areas/ae-waiting-times-and-activity/",
                               # Change X and Y axis labels
                               x = "Period", 
                               y = "Type I Attendances") +
                          theme (axis.ticks = element_blank()) +
                          theme_light() +
                          # Define new y axis breaks (min, max and numbe of breaks between those values)
                          scale_y_continuous(limits=c(1010000, 1400000),n.breaks=12)

TypeI_cont_y_axis

ggsave("plots/06_A&E_Attendances_scale_y_continuous.png", width = 6, height = 4)

# 8. Add a smooth line to the line chart
TypeI_smooth_line   <- AEATT_plot %>% 
  select(period, type_1_Major_att) %>% 
  ggplot(aes(x = period, y = type_1_Major_att)) +
  geom_line(color="#0072CE", size=1,  linetype=1) +
  # Included new geom
  geom_point(fill="#00A9CE",shape=21,show.legend = FALSE) +
  labs(title = "A&E Attendances in England: Type 1 Departments - Major A&E",
       subtitle ="Source: https://www.england.nhs.uk/statistics/statistical-work-areas/ae-waiting-times-and-activity/",
       # Change X and Y axis labels
       x = "Period", 
       y = "Type I Attendances") +
  theme (axis.ticks = element_blank()) +
  theme_light() +
  # Define new y axis breaks (min, max and numbe of breaks between those values)
  scale_y_continuous(limits=c(1010000, 1400000),n.breaks=12) +
  # Add a smooth line to the plot
  geom_smooth()

TypeI_smooth_line

ggsave("plots/07_A&E_Attendances_smooth_line.png", width = 6, height = 4)

# 9 tailor that smooth line
# Parameters we can use with the geom_smooth() function:
# span = 0.3, 

TypeI_smooth_line   <- AEATT_plot %>% 
  select(period, type_1_Major_att) %>% 
  ggplot(aes(x = period, y = type_1_Major_att)) +
  geom_line(color="#0072CE", size=1,  linetype=1) +
  # Included new geom
  geom_point(fill="#00A9CE",shape=21,show.legend = FALSE) +
  labs(title = "A&E Attendances in England: Type 1 Departments - Major A&E",
       subtitle ="Source: https://www.england.nhs.uk/statistics/statistical-work-areas/ae-waiting-times-and-activity/",
       # Change X and Y axis labels
       x = "Period", 
       y = "Type I Attendances") +
  theme (axis.ticks = element_blank()) +
  theme_light() +
  # Define new y axis breaks (min, max and numbe of breaks between those values)
  scale_y_continuous(limits=c(1010000, 1400000),n.breaks=12) +
  # Add a smooth line to the plot
  geom_smooth(span = 0.1, se = TRUE, size = 0.8)

TypeI_smooth_line

ggsave("plots/09_A&E_Attendances_smooth_line_tailored.png", width = 6, height = 4)

# 10. Format Title and Sub title

TypeI_title_format   <- AEATT_plot %>% 
  select(period, type_1_Major_att) %>% 
  ggplot(aes(x = period, y = type_1_Major_att)) +
  geom_line(color="#0072CE", size=1,  linetype=1) +
  # Included new geom
  geom_point(fill="#00A9CE",shape=21,show.legend = FALSE) +
  labs(title = "A&E Attendances in England: Type 1 Departments - Major A&E",
       subtitle ="Source: https://www.england.nhs.uk/statistics/statistical-work-areas/ae-waiting-times-and-activity/",
       # Change X and Y axis labels
       x = "Period", 
       y = "Type I Attendances") +
  theme_light() +
  geom_smooth(se = TRUE, span = 0.1) +
  theme(
    axis.ticks = element_blank(),
    # A value of “plot” means the titles/caption are aligned to the entire plot
    # Apply format to title plot
    plot.title.position = "plot", 
    plot.title = element_text(margin = margin (b=10), colour = "steelblue1", face = "bold"), # Skyblue1 colour
    # Apply format to sub-title
    plot.subtitle = element_text(
      size =8, colour = "palegreen3", face = "bold")
  ) 

TypeI_title_format
ggsave("plots/10_AE_Attendances_format_title_subtitle.png", width = 6, height = 4)