R-格子xyplot-如何将误差线添加到组和汇总行? [英] R - Lattice xyplot - How do you add error bars to groups and summary lines?
问题描述
我发布此问题是因为非常相似的问题到目前为止，这里还没有得到答复.
I'm posting this question because the very similar question here has not been answered until now.
我被要求在描述所有患者价值的xyplot()上绘制整个患者队列的平均值+/- SEM.所使用的数据代表了来自接受手术的患者的术中心血管检查结果.
I have been asked to plot the mean +/- SEM of my whole cohort of patients over the xyplot() that depicts the values of all patients. The data used represents intraoperative cardiovascular findings from patients undergoing surgery.
这是我的data.frame，称为df
dput(df)
structure(list(Name = structure(c(2L, 2L, 2L, 2L, 2L, 2L, 2L,
5L, 5L, 5L, 5L, 5L, 5L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 4L, 4L, 4L, 4L, 4L, 4L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L), .Label = c("DE", "JS", "KG", "MK", "TG", "WT"), class = "factor"),
Time = structure(c(1L, 2L, 3L, 4L, 5L, 7L, 8L, 1L, 2L, 3L,
4L, 7L, 8L, 1L, 2L, 3L, 4L, 5L, 7L, 8L, 1L, 2L, 3L, 4L, 5L,
6L, 7L, 8L, 2L, 3L, 4L, 5L, 7L, 8L, 1L, 2L, 3L, 4L, 5L, 6L,
7L, 8L), .Label = c("T1", "T2", "T3", "T4", "T5", "T6", "T7",
"T8"), class = "factor"), Dobut = structure(c(1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 1L), .Label = c("No", "Yes"
), class = "factor"), DobutDose = c(NA, NA, NA, NA, NA, NA,
NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
4L, 6L, 8L, 8L, 8L, 8L, 8L, NA, NA, NA, NA, NA, NA, NA, NA,
NA, NA, NA, 5L, 5L, NA), CI = c(1.4, 2.3, 1.3, 1.8, 2.1,
2, 2.1, 2.1, 2.3, 1.9, 1.6, 2, 2.4, 2.7, 2.6, 2.7, 2.6, 2.3,
2.4, 2.6, 0.9, 2.5, 2.1, 1.6, 1.5, 1.8, 2, 2, 1.9, 2.1, 2.3,
2, 2.4, 2.3, 2.6, 2.4, 2, 2.2, 1.6, 2.1, 2.5, 2.8), SvO2 = c(57L,
65L, 47L, 45L, 51L, 60L, 56L, 70L, 85L, 75L, 79L, 82L, 73L,
77L, 78L, 73L, 71L, 73L, 80L, 74L, 41L, 66L, 51L, 51L, 49L,
54L, 68L, 48L, 80L, 70L, 71L, 69L, 74L, 79L, 77L, 77L, 75L,
74L, 70L, 79L, 80L, 79L), SVRI = c(4000L, 1983L, 4000L, 2444L,
1981L, 2120L, 2514L, 2971L, 2157L, 3747L, 4300L, 3200L, 2867L,
1778L, 1169L, 1215L, 1262L, 1461L, 1600L, 1692L, 4978L, 1760L,
2019L, 2650L, 2827L, 2356L, 1800L, 2840L, 2063L, 2248L, 1948L,
2160L, 1733L, 2296L, 2677L, 2100L, 2640L, 2655L, 3950L, 2210L,
2848L, 2543L), MAP = c(80L, 65L, 86L, 74L, 67L, 65L, 74L,
90L, 70L, 90L, 96L, 94L, 100L, 82L, 60L, 61L, 62L, 62L, 69L,
71L, 70L, 71L, 77L, 73L, 75L, 77L, 61L, 85L, 65L, 74L, 70L,
67L, 69L, 74L, 92L, 71L, 88L, 93L, 89L, 79L, 97L, 97L), CVP = c(10L,
8L, 21L, 19L, 15L, 12L, 8L, 12L, 8L, 11L, 10L, 14L, 14L,
22L, 22L, 20L, 21L, 20L, 21L, 16L, 14L, 16L, 24L, 20L, 22L,
24L, 16L, 14L, 16L, 15L, 14L, 13L, 17L, 8L, 5L, 8L, 22L,
20L, 20L, 21L, 8L, 8L), PAP = c(23L, 22L, 36L, 36L, 34L,
32L, 22L, 33L, 28L, 36L, 36L, 40L, 37L, 37L, 40L, 35L, 35L,
34L, 38L, 36L, 45L, 43L, 55L, 49L, 52L, 54L, 43L, 47L, 27L,
25L, 23L, 22L, 28L, 21L, 20L, 25L, 33L, 33L, 38L, 35L, 33L,
29L), PCWP = c(15L, 11L, 28L, 26L, 23L, 21L, 11L, 26L, NA,
NA, 25L, 25L, NA, 27L, NA, NA, NA, NA, NA, NA, 30L, NA, NA,
NA, NA, NA, NA, NA, 19L, NA, NA, NA, NA, NA, 16L, NA, NA,
NA, NA, NA, NA, NA)), .Names = c("Name", "Time", "Dobut",
"DobutDose", "CI", "SvO2", "SVRI", "MAP", "CVP", "PAP", "PCWP"
), class = "data.frame", row.names = c(NA, -42L))
现在我为变量CI创建的第一个xyplot看起来像这样
Now the first xyplot I made for the variable CI looks like this
require(lattice)
xyplot(CI~Time, groups=Name, data=df, ty=c("l", "p"),
+ ,xlab="Measurement Time Point",
ylab=expression("CI"~(l/min/m^"2")), main="Cardiac Index")
现在，通过执行以下操作，我能够添加整个队列的均值(黑线)
Now I was able to add the mean (black line) of the whole cohort, by doing the following
xyplot(CI~Time, groups=Name, data=df, ty=c("l", "p"),
panel = function(x, y, ...) {
panel.xyplot(x, y, ...)
panel.linejoin(x, y, horizontal = FALSE,..., col="black", lty=1, lwd=4)
}
,xlab="Measurement Time Point",
ylab=expression("CI"~(l/min/m^"2")), main="Cardiac Index")
现在，我想在平均值的上方/下方添加一条线，以在平均值上添加+/- SE，但我无处可寻.
Now I'd like to add +/- SE to the mean as a line above/below the mean, but nowhere can I find how to do this.
我能做的是使用latticeExtra软件包，如下所示添加黄土线+/- SE，但这不是我要寻找的正确数学函数.我在其中留下了均线以说明两者之间的区别.
What I can do is using the latticeExtra package is add the loess line +/- SE, as below, but that's not the correct mathematical function I'm looking for. I've left the mean line in there to illustrate the difference between the two.
require(latticeExtra)
xyplot(CI~Time, groups=Name, data=df, ty=c("l", "p"),
+ panel = function(x, y, ...) {
+ panel.xyplot(x, y, ...)
+ panel.linejoin(x, y, horizontal = FALSE,..., col="black", lty=1, lwd=4)
+ panel.smoother(x,y,se=TRUE, col.se="grey")
+ }
+ ,xlab="Measurement Time Point",
ylab=expression("CI"~(l/min/m^"2")), main="Cardiac Index")
我已经通过SO和Internet进行了广泛的搜索，但是我找不到合适的功能来做到这一点.
I have performed an extensive search through SO and the internet, but I haven't been able to find the right function to do this.
非常感谢您的帮助！谢谢.
Help is very much appreciated! Thanks.
推荐答案
您可以创建自己的面板函数来绘制+/- SD区域.例如
You could create your own panel function to plot a +/- SD region. For example
#new panel function
panel.se <- function(x, y, col.se=plot.line$col, alpha.se=.25, ...) {
plot.line <- trellis.par.get("plot.line")
xs <- if(is.factor(x)) {
factor(c(levels(x) , rev(levels(x))), levels=levels(x))
} else {
xx <- sort(unique(x))
c(xx, rev(xx))
}
means <- tapply(y,x, mean, na.rm=T)
vars <- tapply(y,x, var, na.rm=T)
Ns <- tapply(!is.na(y),x, sum)
ses <- sqrt(vars/Ns)
panel.polygon(xs, c(means+ses, rev(means-ses)), col=col.se, alpha=alpha.se)
}
然后您可以像使用它
#include new panel function
xyplot(CI~Time, groups=Name, data=df, ty=c("l", "p"),
panel = function(x, y, ...) {
panel.se(x,y, col.se="grey")
panel.xyplot(x, y, ...)
panel.linejoin(x, y, horizontal = FALSE,..., col="black", lty=1, lwd=4)
}
,xlab="Measurement Time Point",
ylab=expression("CI"~(l/min/m^"2")), main="Cardiac Index")
结果
这篇关于R-格子xyplot-如何将误差线添加到组和汇总行?的文章就介绍到这了，希望我们推荐的答案对大家有所帮助，也希望大家多多支持IT屋！
