Ggplot2 Overlay of Barplot and Line Plot

How can a line be overlaid on a bar plot using ggplot2?

Perhaps your sample data aren't representative of the real data you are working with, but there are no lines to be drawn for df2. There is only one value for each x and y value. Here's a modifed version of your df2 with enough data points to construct lines:

df <- data.frame(grp=c("A","A","B","B","C","C"),val=c(1,2,3,1,2,3))
df2 <- data.frame(grp=c("A","A","B","B","C","C"),val=c(1,4,3,5,0,2))

p <- ggplot(df, aes(x=grp, y=val)) 
p <- p + geom_bar(stat="identity", alpha=0.75) 

p + geom_line(data=df2, aes(x=grp, y=val), colour="blue")

Alternatively, if your example data above is correct, you can plot this information as a point with geom_point(data = df2, aes(x = grp, y = val), colour = "red", size = 6). You can obviously change the color and size to your liking.

EDIT: In response to comment

I'm not entirely sure what the visual for a freq polynomial over a histogram is supposed to look like. Are the x-values supposed to be connected to one another? Secondly, you keep referring to wanting lines but your code shows geom_bar() which I assume isn't what you want? If you want lines, use geom_lines(). If the two assumptions above are correct, then here's an approach to do that:

 #First let's summarise df2 by group
 df3 <- ddply(df2, .(grp), summarise, total = sum(val))
>  df3
  grp total
1   A     5
2   B     8
3   C     3

#Second, let's plot df3 as a line while treating the grp variable as numeric

p <- ggplot(df, aes(x=grp, y=val))
p <- p + geom_bar(alpha=0.75, stat = "identity") 
p + geom_line(data=df3, aes(x=as.numeric(grp), y=total), colour = "red")

Overlaying line plot on barplot ggplot -

You need to scale up your Mean_EVI values by 50 to match the ./50 part of your sec.axis call.

Mean_EVI <- c(0.6190386, 0.5208025, 0.6097692, 0.5689, 0.5687068, 0.5663895, 0.5653846, 0.6504931, 0.584727, 0.5799395, 0.617363, 0.581645)

Anopheles_pos <- c(2L, 15L, 12L, 19L, 33L, 42L, 38L, 31L, 54L, 47L, 22L, 15L)

graph <- data.frame(Mean_EVI, Anopheles_pos, Month = 1:12)

ggplot(graph) + 
  geom_col(aes(x = factor(Month, labels = month.name), y = Anopheles_pos), size = 1,
           color = "darkblue", fill = "white") + 
  geom_line(aes(x =  factor(Month, labels = month.name), y = Mean_EVI*50), size = 1.5, 
            color = "red", group = 1) +
  scale_y_continuous(sec.axis = sec_axis(~./50, name = "Mean_EVI")) +
  coord_cartesian(ylim = c(0, 100))

Sample Image

How to plot a combined bar and line plot in ggplot2

Is this what you had in mind?

ratio <- max(feat$Count)/max(feat$CI2)
ggplot(feat) +
  geom_bar(aes(x=Feat, y=Count),stat="identity", fill = "steelblue") +
  geom_line(aes(x=Feat, y=OR*ratio),stat="identity", group = 1) +
  geom_point(aes(x=Feat, y=OR*ratio)) +
  geom_errorbar(aes(x=Feat, ymin=CI1*ratio, ymax=CI2*ratio), width=.1, colour="orange", 
                position = position_dodge(0.05)) +
    scale_y_continuous("Count", sec.axis = sec_axis(~ . / ratio, name = "Odds Ratio"))

Sample Image

Edit: Just for fun with the legend too.

ggplot(feat) +
  geom_bar(aes(x=Feat, y=Count, fill = "Count"),stat="identity") + scale_fill_manual(values="steelblue") +
  geom_line(aes(x=Feat, y=OR*ratio, color = "Odds Ratio"),stat="identity", group = 1) + scale_color_manual(values="orange") +
  geom_point(aes(x=Feat, y=OR*ratio)) +
  geom_errorbar(aes(x=Feat, ymin=CI1*ratio, ymax=CI2*ratio), width=.1, colour="orange", 
                position = position_dodge(0.05)) +
  scale_y_continuous("Count", sec.axis = sec_axis(~ . / ratio, name = "Odds Ratio")) +  
  theme(legend.key=element_blank(), legend.title=element_blank(), legend.box="horizontal",legend.position = "bottom")

Sample Image

Since you asked about adding p values for comparisons in the comments, here is a way you can do that. Unfortunately, because you don't really want to add **all* the comparisons, there's a little bit of hard coding to do.

library(ggplot2)
library(ggsignif)
ggplot(feat,aes(x=Feat, y=Count)) +
  geom_bar(aes(fill = "Count"),stat="identity") + scale_fill_manual(values="steelblue") +
  geom_line(aes(x=Feat, y=OR*ratio, color = "Odds Ratio"),stat="identity", group = 1) + scale_color_manual(values="orange") +
  geom_point(aes(x=Feat, y=OR*ratio)) +
  geom_errorbar(aes(x=Feat, ymin=CI1*ratio, ymax=CI2*ratio), width=.1, colour="orange", 
                position = position_dodge(0.05)) +
  scale_y_continuous("Count", sec.axis = sec_axis(~ . / ratio, name = "Odds Ratio")) +  
  theme(legend.key=element_blank(), legend.title=element_blank(), legend.box="horizontal",legend.position = "bottom") + 
  geom_signif(comparisons = list(c("A","H"),c("B","F"),c("D","E")),
              y_position = c(150,60,40),
              annotation = c("***","***","n.s."))

Sample Image

Overlaying a Bar chart with multiple bars with a line graph with ggplot2 in R

The main problem here is the fill in the ggplot call. Because you have it in ggplot(aes()), it is propagating to both geom_bar and geom_line. If you just set fill = variable inside ggplot(aes()), you wouldn't get the error, but you would have an Total_1 in the legend, which is not what I think you want.

You also don't need to use the df.1.1$ and df.1.2$ inside aes(). You want to put your data in the data argument and then the variables in aes() without calling the data frame again.

Here is a solution.

ggplot(data = df.1.1, aes(x = Month, y = value)) + 
  geom_bar(aes(fill = variable), position = position_dodge(),stat = 'identity') +
  geom_line(data = df.1.2, aes(x=Month, y=value, group=1))

One other note is that you can use geom_col instead of geom_bar with stat='identity'.

ggplot(data = df.1.1, aes(x = Month, y = value)) + 
  geom_col(aes(fill = variable), position = position_dodge()) +
  geom_line(data = df.1.2, aes(x=Month, y=value, group=1))

Combining Bar and Line chart (double axis) in ggplot2

First, scale Rate by Rate*max(df$Response) and modify the 0.9 scale of Response text.

Second, include a second axis via scale_y_continuous(sec.axis=...):

ggplot(df)  + 
    geom_bar(aes(x=Year, y=Response),stat="identity", fill="tan1", colour="sienna3")+
    geom_line(aes(x=Year, y=Rate*max(df$Response)),stat="identity")+
    geom_text(aes(label=Rate, x=Year, y=Rate*max(df$Response)), colour="black")+
    geom_text(aes(label=Response, x=Year, y=0.95*Response), colour="black")+
    scale_y_continuous(sec.axis = sec_axis(~./max(df$Response)))

Which yields:

Sample Image