Could someone please help me in changing colours of specific groups in this error plot.
I want groups with similar "habitat types" to be the same colour.
I.e.,
All Seagrass (hard-bottom) sites to be white.
Seagrass soft-bottom = grey
Mussel = black
After hatch year male/female & Hatch year male/female 2021 are all from MUSSEL dominated sites so I want them to be BLACK as well.
Here is my code:
#### METABOLITE DATA ####
TRIG_rawdata = read.csv("C:\\Users\\o_tru\\OneDrive\\ARP\\Metabolites\\SUSC metabolites_TrueTRIG_2005-2006_2021.csv")
## Create error plot ##
# Combine age and sex to create single ("COHORT") factor (HYF = Hatch Year Female, HYM = Hatch Year Male, AHYF = AFTER Hatch Year Female, AHYM = AFTER Hatch Year Male)
library(dplyr)
SUSC_TRIG = mutate(TRIG_rawdata, Cohort = case_when(Age == "HY" & Sex == "F" ~ "HYF", Age == "HY" & Sex == "M" ~ "HYM", Age == "AHY" & Sex == "F" ~ "AHYF",
Age == "AHY" & Sex == "M" ~ "AHYM"))
# Combine Age, Habitat type , and Cohort
SUSC_TRIG_subset = mutate(SUSC_TRIG, Habitat_Year_Cohort = case_when(Year == "2005" & Habitat.Type == "Seagrass (hard-bottom)" & Cohort == "AHYM" ~ "Seagrass (hard-bottom) 2005",
Year == "2005" & Habitat.Type == "Seagrass (soft-bottom)" & Cohort == "AHYM" ~ "Seagrass (soft-bottom) 2005",
Year == "2005" & Habitat.Type == "Mussel (mixed substrate)" & Cohort == "AHYM" ~ "Mussel (mixed substrate) 2005",
Year == "2006" & Habitat.Type == "Seagrass (hard-bottom)" & Cohort == "AHYM" ~ "Seagrass (hard-bottom) 2006",
Year == "2006" & Habitat.Type == "Seagrass (soft-bottom)" & Cohort == "AHYM" ~ "Seagrass (soft-bottom) 2006",
Year == "2006" & Habitat.Type == "Mussel (mixed substrate)" & Cohort == "AHYM" ~ "Mussel (mixed substrate) 2006",
Year == "2021" & Habitat.Type == "Mussel (mixed substrate)" & Cohort == "AHYF" ~ "After Hatch Year Female 2021",
Year == "2021" & Habitat.Type == "Mussel (mixed substrate)" & Cohort == "AHYM" ~ "After Hatch Year Male 2021",
Year == "2021" & Habitat.Type == "Mussel (mixed substrate)" & Cohort == "HYF" ~ "Hatch Year Female 2021",
Year == "2021" & Habitat.Type == "Mussel (mixed substrate)" & Cohort == "HYM" ~ "Hatch Year Male 2021"))
# Create error plot using R function ggerrorplot() [in ggpubr]
library(ggpubr)
SUSC_TRIG_subset$Month <-factor(SUSC_TRIG_subset$Month, levels=c("Dec", "Mar")) #reorder x-axis
SUSC_TRIG_subset$Habitat_Year_Cohort <- factor(SUSC_TRIG_subset$Habitat_Year_Cohort, levels=c("Seagrass (hard-bottom) 2005","Seagrass (soft-bottom) 2005", "Mussel (mixed substrate) 2005",
"After Hatch Year Male 2021", "After Hatch Year Female 2021", "Hatch Year Male 2021", "Hatch Year Female 2021",
"Seagrass (hard-bottom) 2006","Seagrass (soft-bottom) 2006", "Mussel (mixed substrate) 2006"))
TRIG.plot <- ggerrorplot(SUSC_TRIG_subset, x = "Month", y = "True.TRIG", color = "Habitat_Year_Cohort", desc_stat = "mean_sd", error.plot = "errorbar",
add = "mean")
This is what I tried:
# Change colours of groups of error plot
group.colours <- c("Seagrass (hard-bottom) 2005" = "#FFFFFF", "Seagrass (soft-bottom) 2005" = "#999999", "Mussel (mixed substrate) 2005" = "#000000",
"After Hatch Year Male 2021" = "#000000", "After Hatch Year Female 2021" = "#000000", "Hatch Year Male 2021" = "#000000", "Hatch Year Male 2021 = #000000",
"Seagrass (hard-bottom) 2006" = "#FFFFFF", "Seagrass (soft-bottom) 2006" = "#999999", "Mussel (mixed substrate) 2006" = "#000000")
TRIG.plot <- ggerrorplot(SUSC_TRIG_subset, x = "Month", y = "True.TRIG", color = "Habitat_Year_Cohort",
desc_stat = "mean_sd",
error.plot = "errorbar",
add = "mean") + scale_fill_manual(values=group.colours)
Thank you for your help!!