GGPLOT- how to change default order of BOXPLOT with 3 groups and 3 subgroups

When encountering this problem you can use factor with the variables (both in X variable and the subgroup variable to get them ordered using level=

In this case I think would look like this:

level_orderX <- c("Petit", "Moyens","Grands")
level_order_subgroup <- c("Pesticides", "Medicaments", "Autres MP")

P <- Case1 %>% ggplot(aes(x= factor(River, level=level_orderX), y=newMess, fill=factor(Type, level = level_order_subgroup))) +
  geom_boxplot(position = "dodge2",outlier.shape = 1) +
  scale_y_continuous(trans = 'log10') + 
  stat_boxplot(geom = 'errorbar', lenght=0.5)
  

Also when trying this it gives me a warning for the boxplot saying the lenght isn't used. When haing a boxplot usually the error bar is implied in the wiskers of the plot calculated from the data itself, so I am not sure if the last line of code is really needed? It would be for example for a barplot but maybe not for a boxplot! Hope it helped!

It would be helpful to see your plot as it comes out. If you use 'River' on the x-axis, then it will be ordered by 'River', and 'Type' will be used to colour the bars, although you can change the order of the 'River' groups on the x-axis. If you instead use 'Type' as your x-axis, you can sort it on sub-groups per River.

These examples might be helpful, you can also see this answer described here.

I have data where Session takes values 0, 1 and 2. I also have Group which takes on values 1 and 2.

DG_Means <- summarySE(data = DGUG_All, measurevar = "UG_Deliberation", groupvars = c("Session","Group"))

ggplot(data=DGUG_All, aes(x = factor(Session,level=c(2,1,0)), y = UG_Deliberation, fill = Group, color = Group, Group = Group)) +
  geom_boxplot(alpha = 0.6,color="black") +
  theme_light()

I can also change what goes on the x-axis and what I use for fill, to change this (also, by specifying x = factor(Group,level=c(2,1)) you can decide the order of 'Group' on the x-axis. If you say: x = factor(Group,level=c(1,2)), then the order will change).

ggplot(data=DGUG_All, aes(x = factor(Group,level=c(2,1)), y = UG_Deliberation, fill = Session, color = Session)) +
  geom_boxplot(alpha = 0.6,color="black") +
  theme_light()

Thank you really much for your answer! Unfortunately, it doesn't really reply to my question. Swapping the x and y axis don't solve my problem as I want the order on the x axis to follow the subgroups in any of the two cases.

I thought I added images, I'm sorry. I will add them here. How I would like to have my plot

How my plot look like

So in my example, I would like to have the subgroups sorted together, like this:

type1 type 1 type 1 ->type 2 type 2 type 2 -> type3 type 3 type 3

(so that the colour match together) and on the x axis it would be as follow:

river 1 river 2 river 3 -> river 1 river 2 river 3-> river 1 river 2 river 3

In your examples, I would like to have follow the order of the subgroups so that the subgroup with the same colour are one after the other rather than alternated, therefore in example 1 i would like to have the following sequence of subgroups:

Group 1 Group 2

Therefore on the x asis it will be: session 2 1 0 (Group1) -> Session 2 1 0 (Group2)

In the second example instead, it would be ordered again by subgroups, therefore:

Session 0 Session 1 session 2 (so that all the colour match together) and as a consequence on the x axis it will be (reading from left to right):

factor 1 2 (Session 0) then next subgroup -> factor 1 2 (Session 1) and then the last subgroup -> factor 1 2 (session 2)

I hope I made my question a bit clearer now. I appreciate any kind of help, I'm really stuck with this problem :)