ggplot: modify color scale (only) of existing plot

I have created a bar plot having partially recycling some code from a previous project (the data structure is very nearly identical) which (as expected) has resulted in 5 different coloured bars. However, there is an association between the first 3 bars that I would like to draw attention to by colouring them similarly (e.g. pink, pale red and deep red) while keeping the other 2 bars their present/default colours. I have and would like to maintain other specific characteristics of the code such as keeping the black outline around and the bars and having the error bars also be black in colour. I have tried altering different sections of the code to see if there is a specific element that will allow me to manual set the colour of my bars (e.g. fill=c('pink'...) but this has resulted in disastrous changes to other elements of the plot such as moving all of the error bars into the centre of the plot, changing the naming of the elements in the legend and merging multiple bars on top of each other. Is there a simple way for me to change the colour of these 3 bars using my existing code?

My data is as follows:

emean_Sleep_State<-c('WAKE','SWS','REM','WAKE','SWS','REM','WAKE','SWS','REM','WAKE','SWS','REM','WAKE','SWS','REM')
emean_Treatment<-c('Disturbed_Feed','Disturbed_Feed','Disturbed_Feed','Disturbed_Foot','Disturbed_Foot','Disturbed_Foot','Disturbed_Temp','Disturbed_Temp','Disturbed_Temp','Recovery','Recovery','Recovery','UnDisturbed','UnDisturbed','UnDisturbed')

emean_Means<-c(27.68,52.64,21.36,35.38,47.96,15.59,42.28,45.84,6.03,27.56,52.2,22.36,28.62,52.84,21.01)
emean_SE<-c(3.94,2.99,3.08,3.97,3.01,3.1,3.84,2.91,3.03,2.94,2.34,2.51,5.75,2.92,4.18)

emeanframe<-data.frame(emean_Sleep_State,emean_Treatment,emean_Means,emean_SE)

Estimated_Max_Means_emean<-emeanframe$emean_Means+emeanframe$emean_SE
Estimated_Min_Means_emean<-emeanframe$emean_Means-emeanframe$emean_SE

emeanframe<-data.frame(emean_Sleep_State,emean_Treatment,emean_Means,emean_SE,Estimated_Max_Means_emean,Estimated_Min_Means_emean)

realvalueemean<-apply(emeanframe[,c(3,5,6)],2,FUN=backtransANG)
emeanframe$realmean<-realvalueemean[,1]
emeanframe$realmaxmean<-realvalueemean[,2]
emeanframe$realminmean<-realvalueemean[,3]

If it is of relevance, the function is as follows:

  backtransANG<-function(ANG_value){
  real_value<-(sin(ANG_value/(180/pi)))^2
  return(real_value)}

The code that I used to create my plot is as follows:

emeanplot2<-ggplot(emeanframe,
                   aes(x=emean_Sleep_State,
                       y=realmean,
                       fill=emean_Treatment))+
  geom_col(position='dodge',
           color='black')+
  geom_errorbar(aes(ymin=realminmean,
                    ymax=realmaxmean),
                color='black',width=0.2,position=position_dodge(width=0.9),linewidth=1)+
  scale_x_discrete(limits=c('WAKE','SWS','REM'))+
  labs(x='Sleep State',
       y= 'Proportion of Behaviour',
       color="Type of Night",size=14)+
  ylim(0,1)+
  guides(fill=guide_legend(title='Type of Night'))+
  theme(axis.text.x=element_text(size=12),
        axis.text.y=element_text(size=12),
        axis.title.x=element_text(size=14),
        axis.title.y=element_text(size=14))

I have tried tinkering with elements such as fill=emean_Treatment, and additional elements within geom_col but nothing has yet resulted in my preferred colours even being added to the plot, only a complete mess of the current plot.

You can replace existing scales (in your case the fill-scale) by adding a new scale. Example:

p <- data.frame(x = LETTERS[1:3], y = 1:3) |>
  ggplot(aes(x, y)) + 
  geom_col(aes(fill = x)) +
  ggtitle('old fill colours') +
  scale_fill_manual(values = c(A = 'green', B = 'blue', C = 'red'))


p_new <- p + 
  ggtitle('new fill colours') +
  scale_fill_manual(values = c(A = 'green', B = 'blue', C = 'yellow'))

You can easily achieve the desired fill by applying the same colour three times. Here's how the bars are coloured:

custom_colors <- c("pink", "pink", "pink", "coral2", "darkred")

This line defines a vector custom_colors that specifies the colours for the bars. These colours are assigned to the bars based on their order in the emean_treatment variable in the emeanframe data frame.

In the ggplot() function, the fill aesthetic is still mapped to the emean_Treatment variable. You just add the information about the colours with scale_fill_manual().

emeanplot2 <- ggplot(emeanframe,
                     aes(x = emean_Sleep_State,
                         y = realmean,
                         fill = emean_Treatment)) +
  geom_col(position = "dodge",
           color = "black") +
  geom_errorbar(aes(ymin = realminmean,
                    ymax = realmaxmean),
                color = "black",
                width = 0.2,
                position = position_dodge(width = 0.9),
                linewidth = 1) +
  scale_x_discrete(limits = c("WAKE", "SWS", "REM")) +
  labs(x = "Sleep State",
       y = "Proportion of Behaviour",
       color = "Type of Night",
       size = 14) +
  ylim(0, 1) +
  guides(fill = guide_legend(title = "Type of Night")) +
  theme(axis.text.x = element_text(size = 12),
        axis.text.y = element_text(size = 12),
        axis.title.x = element_text(size = 14),
        axis.title.y = element_text(size = 14)) +
  scale_fill_manual(values = custom_colors)