Thanks a lot in advance for any help

This is my data:

I'm trying to change the order of legend in a graphic that represents species accumulation curve with data shown above. The code that I am using for this is this:

p2 <- ggplot(data = data, aes(x = Samples))  
  geom_point(aes(y = S.est.), shape = 22, fill = "turquoise") 
  geom_point(aes(y = Singletons.Mean), shape = 17, fill = "purple") 
  geom_point(aes(y = Doubletons.Mean)) 
  geom_point(aes(y = Chao.1.Mean), shape = 21, fill = "red") 
  geom_point(aes(y = Jack.1.Mean)) 
  geom_line(aes(y = S.est., colour = "S (est)"), size = 1)   
  geom_line(aes(y = Singletons.Mean, colour="Singletons"), size = 1)  
  geom_line(aes(y = Doubletons.Mean, colour="Doubletons"), size = 1)  
  geom_line(aes(y = Chao.1.Mean, colour = "Chao 1"), size = 1)   
  geom_line(aes(y = Jack.1.Mean, colour = "Jack 1"), size = 1)  
  labs(x = "Sampling days", y = "Number of species")  
  scale_x_continuous(limits = c(1, 12), breaks = c(0, 2, 4, 6, 8, 10, 12))  
  scale_y_continuous(limits = c(0, 200), breaks = c(0, 20, 40, 60, 80, 100, 120, 140, 160, 180, 200))  
  scale_color_manual(name = "Richness estimators ", 
                     values=c("#CC0000","#006600", "#669999", "#00CCCC", 
                              "#660099")) 
  theme_bw()

I have try on doing this with many commands as scale_color_manual, scale_fill_discrete and others but nothing works. It's just doesn't change nothing. The order I want is S, Singl, Doubl, Chao and Jack.

Also, any suggestion that can help me make this graph more aesthetic will be very well received.

Thanks a lot and good night.

CodePudding user response：

For the ordering part of the question, the typical approach is to reshape your data long and make the series be an ordered factor.

Given this data:

my_data <- data.frame(
     Samples = c(1L, 2L, 3L, 4L, 5L),
           S = c(43.92, 63.8, 76.51, 86.25, 94.4),
  Singletons = c(32.04, 33.08, 32.78, 34.27, 36.13),
  Doubletons = c(8.88, 17.87, 18.42, 17.5, 16.44),
       Chao1 = c(101.8, 96.43, 106.6, 120.16, 134.01),
       Jack1 = c(44.1, 84.71, 102.78, 117.02, 128.17)
)

We can reshape the data, define the order of the factor, and plot:

library(tidyverse)
my_data %>%
  pivot_longer(-Samples, names_to = "estimator") %>%
  mutate(estimator = factor(
    estimator,
    levels = c("S", "Singletons", "Doubletons", "Chao1", "Jack1"))) %>%
  ggplot(aes(Samples, value, color = estimator))  
  geom_line()   
  theme_bw()

As a factor, we can further manipulate the estimator order if we want. For instance, adding %>% fct_rev at the end of the "estimator" formula will reverse the order:

... or %>% fct_reorder(value) %>% fct_rev to get them in order of value (median, by default):

CodePudding user response：

If you persist to do it in wide format (I really recommend to do it as @Jon Spring suggest), then we have to change scale_color_manual:

First create two vectors, one with your names in order you like, and then the colors, then add to scale_color_manual:

Example data taken from Jon Spring and adapted a little:

library(ggplot2)

  my_colors <- c("#CC0000","#006600", "#669999", "#00CCCC", "#660099")
  my_labels <- c("S", "Singletons", "Doubletons", "Chao1", "Jack1")

ggplot(data = data, aes(x = Samples))  
  geom_point(aes(y = S), shape = 22, fill = "turquoise") 
  geom_point(aes(y = Singletons), shape = 17, fill = "purple") 
  geom_point(aes(y = Doubletons)) 
  geom_point(aes(y = Chao1), shape = 21, fill = "red") 
  geom_point(aes(y = Jack1)) 
  geom_line(aes(y = S, colour = "S (est)"), size = 1)  
  geom_line(aes(y = Singletons, colour="Singletons"), size = 1)  
  geom_line(aes(y = Doubletons, colour="Doubletons"), size = 1)  
  geom_line(aes(y = Chao1, colour = "Chao 1"), size = 1)   
  geom_line(aes(y = Jack1, colour = "Jack 1"), size = 1)  
  labs(x = "Sampling days", y = "Number of species")  
  scale_x_continuous(limits = c(1, 6), breaks = c(0, 2, 4, 6))  
  scale_y_continuous(limits = c(0, 200), breaks = c(0, 20, 40, 60, 80, 100, 120, 140, 160, 180, 200))  
  scale_color_manual(name = "Richness estimators ",
                     labels = my_labels, 
                     values= my_colors) 
  theme_bw()