R ggplot2:向折线图添加显着性水平 [英] R ggplot2: add significance level to line plot
问题描述
我有以下MWE,其中我使用了多个构面来绘制线图.
I have the following MWE in which I make some line plots with facets.
我的数据在 mymelt
数据框中,并且我想向图添加显着性值,并存储在 pvmelt
数据框中.
My data is in the mymelt
data frame, and I want to add significance values to the plot, stored in the pvmelt
data frame.
我打算使用 geom_text
尝试此操作,但我想知道是否有使用 geom_signif
的更正确方法.
I was going to attempt this using geom_text
, but I am wondering whether there is a more correct way of doing it with geom_signif
.
这是我到目前为止拥有的MWE:
This is the MWE I have so far:
##MWE
library(reshape2)
library(ggplot2)
set.seed(3)
mydf <- data.frame(treatment=rep(c('control','drug'),each=3), time=rep(c('week1','week2','week3'),2), fit1=runif(6, 0, 10), fit2=runif(6, 0, 10))
mymelt <- melt(mydf, measure.vars=c('fit1','fit2'))
mymelt
pvdf <- data.frame(contrast='drug - control', time=c('week1','week2','week3'), pv1=runif(3, 0, 0.075), pv2=runif(3, 0, 0.075))
pvmelt <- melt(pvdf, measure.vars=c('pv1','pv2'))
pvmelt$map.signif <- ifelse(pvmelt$value > 0.05, "", ifelse(pvmelt$value > 0.01,"*", "**"))
pvmelt
png(filename='test.png', height=500, width=800)
print(
ggplot(mymelt, aes(x=time, y=value, group=treatment, col=treatment, shape=treatment)) +
facet_grid(variable~.) +
geom_line(aes(lty=treatment), size=1.5) +
geom_point(alpha=0.5, size=4)
)
dev.off()
mymelt
看起来像这样:
> mymelt
treatment time variable value
1 control week1 fit1 1.680415
2 control week2 fit1 8.075164
3 control week3 fit1 3.849424
4 drug week1 fit1 3.277343
5 drug week2 fit1 6.021007
6 drug week3 fit1 6.043941
7 control week1 fit2 1.246334
8 control week2 fit2 2.946009
9 control week3 fit2 5.776099
10 drug week1 fit2 6.309793
11 drug week2 fit2 5.120159
12 drug week3 fit2 5.050239
pvmelt 看起来像这样:
> pvmelt
contrast time variable value map.signif
1 drug - control week1 pv1 0.040052652 *
2 drug - control week2 pv1 0.041793708 *
3 drug - control week3 pv1 0.065093962
4 drug - control week1 pv2 0.062228152
5 drug - control week2 pv2 0.008358687 **
6 drug - control week3 pv2 0.052776627
我生成的情节就是这样的
The plot I generate is this one:
但是我想要这样的东西,并带有 pvmelt
map.signif信息:
But I want something like this, with pvmelt
map.signif information:
完成它的最好方法是什么?
What would be the best way to accomplish it?
推荐答案
以下内容应创建与您要查找的内容相似的图表:
The following should create a chart similar to what you're looking for:
library(dplyr)
# change pvmelt's variable values to match mymelt's variable values
levels(pvmelt$variable) <- levels(mymelt$variable)
# join data frames
df <- left_join(mymelt,
pvmelt %>% select(time, variable, map.signif),
by = c("time", "variable"))
ggplot(df,
aes(x = time, y = value,
col = treatment, shape = treatment,
group = treatment, lty = treatment,
label = map.signif)) +
facet_grid(variable~ .) +
geom_line(size = 1.5) +
geom_point(alpha = 0.5, size = 4) +
geom_text(aes(y = max(value) + 0.3), # position slightly above highest point
color = "black", size = 10)
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