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Good evening everyone, this is my first post on stack overflow so I hope you'll forgive me for my level of english and if I made some "rules" mistake.
I am working, for a school project, on some cool visualization with ggplot2 on the dataset Covid19.

What I am aiming to do is plotting a curve that is colored regarding a certain factor, here (stay_home_restrictions), and I managed to produce said plot but I'm quite dissatisfied with the colors and would like to change them.

enter image description here

Here is my code :

#libraries  
library(COVID19)  
library(naniar)  
library(ggplot2)  
library(tidyr)  
library(dplyr)  
library(lubridate)  
library(hms)  
library(scales)  
library(RColorBrewer)  

cov1=covid19(level = 1) #Original df  
#Grouping by country and keeping what I feel useful  
cov1conf2=cov1%>%
  group_by(administrative_area_level_1)%>%
   select(date,deaths,confirmed,recovered,people_vaccinated,people_fully_vaccinated,workplace_closing,
     cancel_events,gatherings_restrictions,transport_closing,stay_home_restrictions,
     internal_movement_restrictions,international_movement_restrictions,facial_coverings,population)%>%
  mutate(confirmed_pct=round((confirmed/population)*100, 5),deaths_pct=round((deaths/population)*100, 5),
     people_vaccinated_pct=round((people_vaccinated/population)*100, 5),
     people_fully_vaccinated_pct=round((people_fully_vaccinated/population)*100, 5))

#reducing number of country to those I chose to study  
cntry_of_interest=cov1conf2%>%
  filter(administrative_area_level_1 %in% c("United States","France","China","Japan"))

#Data from France  
France <-cntry_of_interest%>%
  filter(administrative_area_level_1=="France")%>%
  mutate(day=format(date,"%d"),month = format(date, "%m"), year = format(date, "%Y"))
#Daily number of confirmed cases and deaths  
France_daily<-France%>% 
  mutate(daily_confirmed=c(France$confirmed[1],diff(confirmed)),
         daily_deaths=c(France$deaths[1],diff(deaths)))%>%
  group_by(year)

#Year 2020  
F2020 = France_daily%>%filter(year==2020)
#Plot code !  
plot<-ggplot(F2020,aes(x = date , y = daily_confirmed))+ 
  geom_line(color=as.factor(abs(F2020$stay_home_restrictions)+1))+
  scale_fill_brewer(palette="Set1")+
  scale_x_date(date_breaks = '1 month', 
           labels = date_format("%b-%y"))+
  labs(title = "Percentage of cummulative number of cases in France",
   x = "Date",
   y = "percentage of confirmed cases",
   fill= "stay_home_restrictions")

plot

You'll tell me that this post already exists and that I just need to add a scale_fill_manual but the thing is that my color=as.factor(stay_home_restrictions) is mapped in my geom_line() and the programm just refuses to change the colors with either scale_fill_manual or scale_color_brewer.

I didn't put my color=as.factor(stay_home_restrictions) in the main ggplot2 object (not sure it is called that way) because this would render a plot of 3 superimposed continuous curves (1 for each value of my factor) ! See : Why i didn't put the color=as.factor in main aes

What should I do in order to change the color of the first plot? Thank by advance for your kind support,

DaveArmstrong
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Dataneko
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1 Answers1

1

The issue with your code is that

  • scale_fill_xxx will not have any effect as you use color, i.e. switch to scale_color_xxx.

  • however, scale_color_xxx will only have an effect if you map on the color aesthetic, i.e. use aes(color = as.factor(abs(stay_home_restrictions) + 1))

  • additionally, to prevent that your data will be splitted when mapping on the color aes we have to add the group aesthetic. To this end I map the constant 1 on the group aes.

library(COVID19)
library(ggplot2)
library(dplyr)
library(scales)
library(RColorBrewer)

ggplot(F2020, aes(x = date, y = daily_confirmed)) +
  geom_line(aes(color = as.factor(abs(stay_home_restrictions) + 1), group = 1)) +
  scale_color_brewer(palette = "Set1") +
  scale_x_date(
    date_breaks = "1 month",
    labels = date_format("%b-%y")
  ) +
  labs(
    title = "Percentage of cummulative number of cases in France",
    x = "Date",
    y = "percentage of confirmed cases",
    fill = "stay_home_restrictions"
  ) +
  guides(color = "none")

plot
#> Warning: Removed 2 row(s) containing missing values (geom_path).

stefan
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