ggplot2, Ordering y axis

Question

I have the below data.frame called df. My problem has to do with the order on the y-axis. I want that the names on the y-axis are ordered according to the variable depth.

If I do this:

ggplot(df,aes(x=factor(name),y=depth)) + geom_bar(stat='identity') + coord_flip() + labs(y='depth',x='species')

I got graph1 below which is not ordered. Therefore I followed the instructions found here, I ordered the levels of my factor name according to depth:

df2=df[order(df$depth),]
df2$name=factor(df2$name,levels=df2$name)
ggplot(df2,aes(x=factor(name),y=depth)) + geom_bar(stat='identity') + coord_flip() + labs(y='depth',x='species')

I got Graph2 below. But the next step for me was to color the bars differently depending on the Mut variable.

ggplot(df2,aes(x=factor(name),y=depth)) + geom_bar(stat='identity',data=subset(df2,df2$Mut==2),fill='red') + geom_bar(stat='identity',data=subset(df2,df2$Mut==1),fill='blue') + coord_flip() + labs(y='depth',x='species')

And I got Graph3 which is not ordered anymore!!

How can I produce graph3 respecting the order displayed in graph2

                    name depth Mut            x
25  A_rubrocinctus_GA070     8   2 -0.033318659
9      A_omanensis_GA051    10   2 -0.020387101
4  A_latifasciatus_GA083    12   1 -0.005645811
27      A_frenatus_GA068    12   1 -0.024190876
13       A_percula_GA017    15   1  0.034591721
14       A_percula_GA039    15   2  0.034591721
15       A_percula_GA053    15   2  0.034591721
16     A_ocellaris_GA009    15   1  0.052042539
17     A_ocellaris_GA021    15   1  0.052042539
24     A_ephippium_GA057    15   2 -0.016859412
20   P_biaculeatus_GA008    16   1 -0.014466403
21   P_biaculeatus_GA025    16   1 -0.014466403
22   P_biaculeatus_GA065    16   1 -0.014466403
23     A_melanopus_GA034    18   2 -0.026915545
26     A_melanopus_GA012    18   2 -0.026915545
12  A_sandaracinos_GA018    20   1  0.055839755
6       A_nigripes_GA055    25   1  0.023420045
8          A_sebae_GA029    25   1  0.021767793
11   A_akallopisos_GA067    25   1  0.043272525
28   A_akallopisos_GA072    25   1  0.043272525
34     A_akindynos_GA032    25   1 -0.020707141
1       A_polymnus_GA004    30   1  0.030902254
3        A_allardi_GA033    30   1 -0.020277664
5      A_bicinctus_GA036    30   1 -0.025354572
7       A_polymnus_GA019    30   1  0.030902254
32  A_chrysopterus_GA040    30   1 -0.022402365
33  A_chrysopterus_GA031    30   1 -0.022402365
35   A_perideraion_GA020    38   1  0.052830132
36   A_perideraion_GA015    38   1  0.052830132
2     A_tricinctus_GA058    40   1 -0.016230301
18  A_chrysogaster_GA080    40   1  0.012608835
19  A_chrysogaster_GA077    40   1  0.012608835
10   A_latezonatus_GA023    45   1 -0.010718845
31    A_mccullochi_GA056    45   1 -0.031664307
29       A_clarkii_GA044    60   1 -0.014474658
30       A_clarkii_GA010    60   1 -0.014474658

Graph1 Graph2 Graph3 Thank you!

Answer 1

As you have variable Mut in your data that determines to which level each observation belongs, you don't need to use geom_bar() twice with subset. Just add fill=factor(Mut) inside the aes() and use df2 with ordered data. Bars will be in correct order and color made automatically.

ggplot(df2,aes(x=factor(name),y=depth,fill=factor(Mut))) + 
     geom_bar(stat='identity') + 
     coord_flip() + labs(y='depth',x='species')

The same result can be achieved with original dataframe df and function reorder() inside aes() for x values.

ggplot(df,aes(x=reorder(name,depth),y=depth,fill=factor(Mut))) + 
     geom_bar(stat='identity') + 
     coord_flip() + labs(y='depth',x='species')