Changing colours of bars in ggplot2

to remove the expansion around the axis limits change your scale_y_* to

scale_y_continuous(trans = "log10",expand = c(0,0))

write your selections as code :

mycols <- c(C1in1 = "midnight blue",
C1In2 = "blue", 
C1Out = "lightblue",
C2In = "red", 
C2Out = "pink", 
C3In = "darkgreen",
C3Out = "lightgreen")

then use that in a scale_fill_*

 + scale_fill_manual(values=mycols)