问题
I am not a Pro R user but I already tried multiple things and can't find a solution to the problem.
I created a bar graph for 2x2 ANOVA including error bars, APA theme and custom colors based on this website: https://sakaluk.wordpress.com/2015/08/27/6-make-it-pretty-plotting-2-way-interactions-with-ggplot2/ It works nicely but the y-axis starts at 0 although my scale only ranges from 1 - 7. I am trying to adapt the axis but I get strange errors.
This is what I did:
# see https://sakaluk.wordpress.com/2015/08/27/6-make-it-pretty-plotting-2-way-interactions-with-ggplot2/
interactionMeans(anova.2)
plot(interactionMeans(anova.2))
#using ggplot
install.packages("ggplot2")
library(ggplot2)
# create factors with value
GIFTSTUDY1DATA$PRICE <- ifelse (Scenario == 3 | Scenario == 4, 1, -1 )
table(GIFTSTUDY1DATA$PRICE)
GIFTSTUDY1DATA$PRICE <- factor(GIFTSTUDY1DATA$PRICE, levels = c(-1, +1),
labels = c("2 expensive", "1 inexpensive"))
GIFTSTUDY1DATA$AFFECT <- ifelse (Scenario == 1 | Scenario == 3, -1, +1 )
table(GIFTSTUDY1DATA$AFFECT)
GIFTSTUDY1DATA$AFFECT <- factor(GIFTSTUDY1DATA$AFFECT,
levels = c(-1,1),
labels = c("poor", "rich"))
# get descriptives
dat2 <- describeBy(EVALUATION,list(GIFTSTUDY1DATA$PRICE,GIFTSTUDY1DATA$AFFECT),
mat=TRUE,digits=2)
dat2
names(dat2)[names(dat2) == 'group1'] = 'Price'
names(dat2)[names(dat2) == 'group2'] = 'Affect'
dat2$se = dat2$sd/sqrt(dat2$n)
# error bars +/- 1 SE
limits = aes(ymax = mean + se, ymin=mean - se)
dodge = position_dodge(width=0.9)
# set layout
apatheme=theme_light()+
theme(panel.grid.major=element_blank(),
panel.grid.minor=element_blank(),
panel.border=element_blank(),
axis.line=element_line(),
text=element_text(family='Arial'))
#plot
p=ggplot(dat2, aes(x = Affect, y = mean, fill = Price))+
geom_bar(stat='identity', position=dodge)+
geom_errorbar(limits, position=dodge, width=0.15)+
apatheme+
ylab('mean gift evaluatoin')+
scale_fill_manual(values=c("yellowgreen","skyblue4"))
p
Which gives me this figure:
https://i.stack.imgur.com/MwdVo.png
Now, if I try to change the y-axis using ylim or scale_y_continous
p + ylim(1,7)
p + scale_y_continuous(limits = c(1,7))
I get a graph with the y-axis as wanted but no bars and an error message stating
Removed 4 rows containing missing values (geom_bar).
https://i.stack.imgur.com/p66H8.png
Using
p + expand_limits(y=c(1,7))
p
changes the upper end of the y-axis but still includes the zero!
What am I doing wrong? Do I have to start all over without using geom_bar? Thanks in advance.
回答1:
I have encountered a similar problem which was solved by replacing
scale_y_continuous(limits = c() with
coord_cartesian(ylim = c())
I think this might work for you.
Here is an example:
library(tidyverse)
ggplot(mtcars,aes(factor(am),hp)) +
geom_bar(stat = "identity") +
coord_cartesian(ylim = c(1000,3000))
Also see link: Google R Discussion
回答2:
While Magnus Nordmo's answer is helpful, I would like to add the reason why ggplot2 behaves this way.
Consider the following plot (friendly reminder that geom_col() is shorthand for geom_bar(stat = "identity")):
df <- data.frame(x = letters[1:7],
y = 1:7)
g <- ggplot(df, aes(x, y)) +
geom_col()
g
You can clearly see that the bars look like rectangles. Checking the underlying plot data, confirms that the bars are parameterised as rectangles with xmin/xmax/ymin/ymax parametrisation:
> layer_data(g)
x y PANEL group ymin ymax xmin xmax colour fill size linetype alpha
1 1 1 1 1 0 1 0.55 1.45 NA grey35 0.5 1 NA
2 2 2 1 2 0 2 1.55 2.45 NA grey35 0.5 1 NA
3 3 3 1 3 0 3 2.55 3.45 NA grey35 0.5 1 NA
4 4 4 1 4 0 4 3.55 4.45 NA grey35 0.5 1 NA
5 5 5 1 5 0 5 4.55 5.45 NA grey35 0.5 1 NA
6 6 6 1 6 0 6 5.55 6.45 NA grey35 0.5 1 NA
7 7 7 1 7 0 7 6.55 7.45 NA grey35 0.5 1 NA
Now consider the following plot:
g2 <- ggplot(df, aes(x, y)) +
geom_col() +
scale_y_continuous(limits = c(1, 7))
This one is empty, and reflects the case you have posted. Inspecting the underlying data yields the following:
> layer_data(g2)
y x PANEL group ymin ymax xmin xmax colour fill size linetype alpha
1 1 1 1 1 NA 1 0.55 1.45 NA grey35 0.5 1 NA
2 2 2 1 2 NA 2 1.55 2.45 NA grey35 0.5 1 NA
3 3 3 1 3 NA 3 2.55 3.45 NA grey35 0.5 1 NA
4 4 4 1 4 NA 4 3.55 4.45 NA grey35 0.5 1 NA
5 5 5 1 5 NA 5 4.55 5.45 NA grey35 0.5 1 NA
6 6 6 1 6 NA 6 5.55 6.45 NA grey35 0.5 1 NA
7 7 7 1 7 NA 7 6.55 7.45 NA grey35 0.5 1 NA
You can see that the ymin column is replaced by NAs. This behaviour depends on the oob (out-of-bounds) argument of scale_y_continuous(), which defaults to the scales::censor() function. This censors (replaces with NA) any values that are outside the axis limits, which includes the 0 which should be the ymin column. As a consequence, the rectangles can't be drawn.
There are two ways to work around this. One candidate is indeed as Magnus suggested to use the ylim argument in the coord_cartesian() function:
ggplot(df, aes(x, y)) +
geom_col() +
coord_cartesian(ylim = c(1, 7))
Specifying the limits inside a coord_* function causes the graphical objects to be clipped. You can see this in action when you turn the clipping off:
ggplot(df, aes(x, y)) +
geom_col() +
coord_cartesian(ylim = c(1, 7), clip = "off")
The other option is to use an alternative oob argument in the scale_y_continuous, for example scales::squish:
g3 <- ggplot(df, aes(x, y)) +
geom_col() +
scale_y_continuous(limits = c(1, 7),
oob = scales::squish)
g3
What this does, is that it replaces any value outside the limits by the nearest limit, e.g. the ymin of 0 becomes 1:
> layer_data(g3)
y x PANEL group ymin ymax xmin xmax colour fill size linetype alpha
1 1 1 1 1 1 1 0.55 1.45 NA grey35 0.5 1 NA
2 2 2 1 2 1 2 1.55 2.45 NA grey35 0.5 1 NA
3 3 3 1 3 1 3 2.55 3.45 NA grey35 0.5 1 NA
4 4 4 1 4 1 4 3.55 4.45 NA grey35 0.5 1 NA
5 5 5 1 5 1 5 4.55 5.45 NA grey35 0.5 1 NA
6 6 6 1 6 1 6 5.55 6.45 NA grey35 0.5 1 NA
7 7 7 1 7 1 7 6.55 7.45 NA grey35 0.5 1 NA
Another thing you could do is provide a custom function to the oob argument, that simply returns it's input. Since by default, clipping is on, this reflects the coord_cartesian(ylim = c(1,7)) case:
ggplot(df, aes(x, y)) +
geom_col() +
scale_y_continuous(limits = c(1, 7),
oob = function(x, ...){x})
I hope this clarified what is going on here.
来源：https://stackoverflow.com/questions/58954151/problems-adapting-the-y-axis-to-2x2-anova-bargraph-using-r-and-ggplot