[英]Quantile calculations using R and GraphPad Prism
I'm new in R. Before using R, I used GraphPad Prism 7.0. 我是R语言的新手。在使用R语言之前,我使用了GraphPad Prism 7.0。 Só now I'm trying to compare both as data processors.
现在,我正在尝试将两者作为数据处理器进行比较。 I founded a difference in the quantile calculations, so anyone know why they are differents??
我在分位数计算中发现了差异,所以有人知道为什么它们是不同的吗?
In R i have 在R我有
par(pty="s", cex.axis=1, las=1, cex.lab=1)
a1=c(22.02, 23.83, 26.67, 25.38, 25.49, 23.50, 25.90, 24.89, 25)
a2=c(21.49, 22.67, 24.62, 24.18, 22.78, 22.56, 24.46, 23.79, 25)
a3=c(20.33, 21.67, 24.67, 22.45, 22.29, 21.95, 20.49, 21.81, 25)
boxplot(a1,a2,a3, names=c("a1","a2","a3"), ylab="Valor", ylim=c(20,28))
And the quantiles for a3 are a3的分位数是
quantile(a3)
0% 25% 50% 75% 100%
20.33 21.67 21.95 22.45 25.00
Plotting the same data in GraphPad Prism: 在GraphPad Prism中绘制相同的数据:
Graph Family: Column Box & whiskers Plot: tukey 图族:圆柱盒和晶须图:tukey
I get 我懂了
And the quantiles are 分位数是
Why they are differents (Particulary a3)?? 为什么它们不同(特别是a3)?
Why R recognize 4 outliers in a3 and GraphPad does not? 为什么R在a3中识别出4个离群值而GraphPad无法识别?
Suggestions?? 建议?
As @lmo says, R has many ways to calculate quantiles. 正如@lmo所说,R有许多计算分位数的方法。 By default, R uses the
type=7
. 默认情况下,R使用
type=7
。 GraphPad uses a method equivalent to type=6
in R. So the way I founded was GraphPad使用等效于R中
type=6
的方法。所以我建立的方式是
par(pty="s", cex.axis=1, las=1, cex.lab=1)
a1=c(22.02, 23.83, 26.67, 25.38, 25.49, 23.50, 25.90, 24.89, 25)
a2=c(21.49, 22.67, 24.62, 24.18, 22.78, 22.56, 24.46, 23.79, 25)
a3=c(20.33, 21.67, 24.67, 22.45, 22.29, 21.95, 20.49, 21.81, 25)
boxplot(
quantile(a1,type=6),
quantile(a2,type=6),
quantile(a3,type=6),
names=c("a1","a2","a3"), ylab="Valor", ylim=c(20,28))
And 和
> quantile(a1,type=6)
0% 25% 50% 75% 100%
22.020 23.665 25.000 25.695 26.670
> quantile(a2,type=6)
0% 25% 50% 75% 100%
21.490 22.615 23.790 24.540 25.000
> quantile(a3,type=6)
0% 25% 50% 75% 100%
20.33 21.08 21.95 23.56 25.00
Same as GraphPad 与GraphPad相同
Answering the question how to use different quantile calculations in a boxplot: 回答如何在箱图中使用不同的分位数计算的问题:
This is easy with ggplot2. 使用ggplot2很容易。
DF <- data.frame(a1, a2, a3)
DF <- stack(DF)
quants <- tapply(DF$values, list(DF$ind), quantile, type = 6)
quants <- as.data.frame(do.call(rbind, quants))
quants$g <- rownames(quants)
library(ggplot2)
ggplot(quants, aes(x = g, lower = `25%`,
middle = `50%`, upper = `75%`,
ymin = `0%`, ymax = `100%`)) +
geom_boxplot(stat = "identity")
You can then customize this plot further as explained in many ggplot2 tutorials. 然后,您可以按照许多ggplot2教程中的说明进一步自定义此图。
PS: However, I would use R's default boxplot stats since these try to reproduce Tukey's boxplot. PS:但是,我将使用R的默认箱形图统计信息,因为它们试图重现Tukey的箱形图。
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