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ons_plots.R
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ons_plots.R
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################################################################################
# Description: Script to plot TPP & ONS data for deaths, imd, sex and age
#
# Input: /output/tables/ethnic_group.csv
#
# Refactors 5 group ethnicity to match the 2011 census groups
#
# output: output/ons/ethnicity_count.png
# output/ons/ethnicity_count_eng.png
# output/ons/ethnicity_16_count.png
# output/ons/ethnicity_16_count_eng.png
#
# Author: Colm D Andrews
# Date: 14/07/2022
#
################################################################################
library(tidyverse)
library(scales)
library(readr)
library(ggpubr)
library(ggsci)
fs::dir_create(here::here("output", "ons"))
fs::dir_create(here::here("output", "ons", "na_removed"))
############### ethnicity with NA
# # read ethnicity produced by combine_ONS.R
# ethnicity <-
# read_csv(here::here("output", "ons", "ethnic_group_registered.csv"))
#
# ethnicity_2011 <-
# read_csv(here::here("output", "ons", "ethnic_group_2011_registered.csv"))
#
# ## use ethnicity_2011 for 5 group and ethnicity for 16 group
# ethnicity_plot <- ethnicity_2011 %>%
# filter(region != "England", group == "5") %>%
# ggplot(aes(x = Ethnic_Group, y = percentage, fill = cohort)) +
# geom_bar(stat = "identity", position = "dodge") +
# facet_wrap( ~ region) +
# theme_classic() +
# theme(text = element_text(size = 20)) +
# theme(axis.text.x = element_text(
# size = 20,
# hjust = 0,
# vjust = 0
# )) +
# coord_flip() +
# xlab("") + ylab("Percentage of all ethnicities")
#
#
#
# ggsave(
# filename = here::here("output", "ons", "ethnicity_count.png"),
# ethnicity_plot,
# dpi = 600,
# width = 45,
# height = 30,
# units = "cm"
# )
#
#
#
# ethnicity_plot_eng <- ethnicity_2011 %>%
# filter(region == "England", group == "5") %>%
# ggplot(aes(x = Ethnic_Group, y = percentage, fill = cohort)) +
# geom_bar(stat = "identity", position = "dodge") +
# theme_classic() +
# theme(text = element_text(size = 20)) +
# theme(axis.text.x = element_text(
# size = 20,
# hjust = 0,
# vjust = 0
# )) +
# coord_flip() +
# xlab("") + ylab("Percentage of all ethnicities")
#
# ggsave(
# filename = here::here("output", "ons", "ethnicity_count_eng.png"),
# ethnicity_plot_eng,
# dpi = 600,
# width = 30,
# height = 30,
# units = "cm"
# )
#
#
# ethnicity_plot16 <- ethnicity %>%
# filter(region != "England", group == "16") %>%
# ggplot(aes(x = Ethnic_Group, y = percentage, fill = cohort)) +
# geom_bar(stat = "identity", position = "dodge") +
# facet_wrap( ~ region) +
# theme_classic() +
# theme(text = element_text(size = 20)) +
# theme(axis.text.x = element_text(
# size = 20,
# hjust = 0,
# vjust = 0
# )) +
# coord_flip() +
# xlab("") + ylab("Percentage of all ethnicities")
#
# ggsave(
# filename = here::here("output", "ons", "ethnicity_16_count.png"),
# ethnicity_plot16,
# dpi = 600,
# width = 45,
# height = 30,
# units = "cm"
# )
#
# ethnicity_plot16_eng <- ethnicity %>%
# filter(region == "England", group == "16") %>%
# ggplot(aes(x = Ethnic_Group, y = percentage, fill = cohort)) +
# geom_bar(stat = "identity", position = "dodge") +
# theme_classic() +
# theme(text = element_text(size = 20)) +
# theme(axis.text.x = element_text(
# size = 20,
# hjust = 0,
# vjust = 0
# )) +
# coord_flip() +
# xlab("") + ylab("Percentage of all ethnicities")
#
# ggsave(
# filename = here::here("output", "ons", "ethnicity_16_count_eng.png"),
# ethnicity_plot16_eng,
# dpi = 600,
# width = 30,
# height = 30,
# units = "cm"
# )
#
####### NA removed
# read ethnicity produced by combine_ONS.R
ethnicity_na <-
read_csv(here::here("output", "ons", "ethnic_group_NA_registered.csv")) %>%
mutate(cohort = fct_relevel(cohort, "ONS", "CTV3","SNOMED","PRIMIS"))
ethnicity_na_2011 <-
read_csv(here::here("output", "ons", "ethnic_group_2011_NA_registered.csv")) %>%
mutate(cohort = fct_relevel(cohort, "ONS", "CTV3","SNOMED","PRIMIS"))
## use ethnicity_2011 for 5 group and ethnicity for 16 group
# 16 group NA removed
ethnicity_plot16_eng_na <- ethnicity_na %>%
filter(region == "England", group == "16") %>%
ggplot(aes(x = Ethnic_Group, y = percentage, fill = cohort)) +
geom_bar(stat = "identity", position = "dodge") +
theme_classic() +
theme(text = element_text(size = 20)) +
theme(axis.text.x = element_text(
size = 20,
hjust = 0,
vjust = 0
)) +
coord_flip() + scale_fill_lancet() +
xlab("") + ylab("\nPercentage of all ethnicities")
ggsave(
filename = here::here(
"output",
"ons",
"na_removed",
"ethnicity_16_count_eng_na.png"
),
ethnicity_plot16_eng_na,
dpi = 600,
width = 30,
height = 30,
units = "cm"
)
## create difference in percentage between ONS and TPP (for plotting)
ethnicity_plot_na_2011_diff <- ethnicity_na_2011 %>%
group_by(Ethnic_Group,region,group) %>%
arrange(cohort) %>%
mutate(diff = percentage - first(percentage))
## 5 group ethnicity plot NA removed for Regions
ethnicity_plot_na <- ethnicity_plot_na_2011_diff %>%
filter(region != "England", group == "5") %>%
ggplot(aes(x = Ethnic_Group, y = percentage, fill = cohort)) +
geom_bar(stat = "identity", position = "dodge") +
facet_wrap( ~ region) +
theme_classic() +
theme(text = element_text(size = 20)) +
theme(axis.text.x = element_text(
size = 12,
hjust = 0.75,
vjust = 0
)) +
coord_flip() + scale_fill_lancet() +
xlab("") + ylab("\nPercentage of all ethnicities") +
theme(legend.position="bottom",
legend.title=element_blank()) +
geom_text(aes(x=Ethnic_Group,y=percentage,label=ifelse(cohort=="ONS","",paste0(round(diff,digits =1),"%"))), size=3.4, position =position_dodge(width=0.9), vjust=0.3,hjust = -0.2)
ggsave(
filename = here::here("output", "ons", "na_removed", "ethnicity_count_na.png"),
ethnicity_plot_na,
dpi = 600,
width = 50,
height = 30,
units = "cm"
)
## 5 group ethnicity plot NA removed for England
ethnicity_plot_eng_na <- ethnicity_plot_na_2011_diff %>%
filter(region == "England", group == "5") %>%
ggplot(aes(x = Ethnic_Group, y = percentage, fill = cohort)) +
geom_bar(stat = "identity", position = "dodge") +
theme_classic() +
theme(text = element_text(size = 20)) +
theme(axis.text.x = element_text(
size = 20,
hjust = 0,
vjust = 0
)) +
coord_flip() + scale_fill_lancet() +
xlab("") + ylab("\nPercentage of all ethnicities") +
theme(legend.position="bottom",
legend.title=element_blank()) +
geom_text(aes(x=Ethnic_Group,y=percentage,label=ifelse(cohort=="ONS","",paste0(round(diff,digits =1),"%"))), size=3.4, position =position_dodge(width=0.9), vjust=0.3 ,hjust = -0.2)
ggsave(
filename = here::here(
"output",
"ons",
"na_removed",
"ethnicity_count_eng_na.png"
),
ethnicity_plot_eng_na,
dpi = 600,
width = 30,
height = 15,
units = "cm"
)
# ## 16 group ethnicity plot NA removed for England
# ethnicity_plot16_na <- ethnicity_na %>%
# filter(region != "England", group == "16") %>%
# ggplot(aes(x = Ethnic_Group, y = percentage, fill = cohort)) +
# geom_bar(stat = "identity", position = "dodge") +
# facet_wrap( ~ region) +
# theme_classic() +
# theme(text = element_text(size = 20)) +
# theme(axis.text.x = element_text(
# size = 20,
# hjust = 0,
# vjust = 0
# )) +
# coord_flip() + scale_fill_lancet() +
# xlab("") + ylab("\nPercentage of all ethnicities")
#
#
# ggsave(
# filename = here::here("output", "ons", "na_removed", "ethnicity_16_count_na.png"),
# ethnicity_plot16_na,
# dpi = 600,
# width = 45,
# height = 30,
# units = "cm"
# )
#
#
# ##### remove white / white british
# ethnicity_plot_eng_nw <- ethnicity_na_2011 %>%
# filter(region == "England",Ethnic_Group!="White", group == "5") %>%
# ggplot(aes(x = Ethnic_Group, y = percentage, fill = cohort)) +
# geom_bar(stat = "identity", position = "dodge") +
# theme_classic() +
# theme(text = element_text(size = 20)) +
# theme(axis.text.x = element_text(
# size = 20,
# hjust = 0,
# vjust = 0
# )) +
# coord_flip() + scale_fill_lancet() +
# xlab("") + ylab("\nPercentage of all ethnicities")
#
# ggsave(
# filename = here::here("output", "ons", "ethnicity_count_eng_nw.png"),
# ethnicity_plot_eng_nw,
# dpi = 600,
# width = 30,
# height = 30,
# units = "cm"
# )
#
# ethnicity_plot_nw <- ethnicity_na_2011 %>%
# filter(region != "England",Ethnic_Group!="White" ,group == "5") %>%
# ggplot(aes(x = Ethnic_Group, y = percentage, fill = cohort)) +
# geom_bar(stat = "identity", position = "dodge") +
# facet_wrap( ~ region) +
# theme_classic() +
# theme(text = element_text(size = 20)) +
# theme(axis.text.x = element_text(
# size = 20,
# hjust = 0,
# vjust = 0
# )) +
# coord_flip() + scale_fill_lancet() +
# xlab("") + ylab("\nPercentage of all ethnicities")
#
# ggsave(
# filename = here::here("output", "ons", "ethnicity_count_nw.png"),
# ethnicity_plot_nw,
# dpi = 600,
# width = 45,
# height = 30,
# units = "cm"
# )
#
# ethnicity_plot16_nw <- ethnicity_na %>%
# filter(region != "England",Ethnic_Group!="White British", group == "16") %>%
# ggplot(aes(x = Ethnic_Group, y = percentage, fill = cohort)) +
# geom_bar(stat = "identity", position = "dodge") +
# facet_wrap( ~ region) +
# theme_classic() +
# theme(text = element_text(size = 20)) +
# theme(axis.text.x = element_text(
# size = 20,
# hjust = 0,
# vjust = 0
# )) +
# coord_flip() + scale_fill_lancet() +
# xlab("") + ylab("\nPercentage of all ethnicities")
#
# ggsave(
# filename = here::here("output", "ons", "ethnicity_16_count_nw.png"),
# ethnicity_plot16_nw,
# dpi = 600,
# width = 45,
# height = 30,
# units = "cm"
# )
#
# ethnicity_plot16_eng_nw <- ethnicity_na %>%
# filter(region == "England",Ethnic_Group!="White British", group == "16") %>%
# ggplot(aes(x = Ethnic_Group, y = percentage, fill = cohort)) +
# geom_bar(stat = "identity", position = "dodge") +
# theme_classic() +
# theme(text = element_text(size = 20)) +
# theme(axis.text.x = element_text(
# size = 20,
# hjust = 0,
# vjust = 0
# )) +
# coord_flip() + scale_fill_lancet() +
# xlab("") + ylab("\nPercentage of all ethnicities")
#
# ggsave(
# filename = here::here("output", "ons", "ethnicity_16_count_eng_nw.png"),
# ethnicity_plot16_eng_nw,
# dpi = 600,
# width = 30,
# height = 30,
# units = "cm"
# )
#
#
#
# ethnicity_5_16 <-
# ggarrange(
# ethnicity_plot_eng_na,
# ethnicity_plot16_eng_na,
# labels = c("A", "B"),
# ncol = 1,
# nrow = 2,
# common.legend = T
# )
#
# ggsave(
# filename = here::here("output", "ons", "ethnicity_5_16_comb.png"),
# ethnicity_5_16,
# dpi = 600,
# width = 30,
# height = 45,
# units = "cm"
# )