[英]Compute and plot pairwise distances using dist in R
I have a dataframe with 4 columns.我有一个包含 4 列的数据框。
set.seed(123)
df <- data.frame(A = round(rnorm(1000, mean = 1)),
B = rpois(1000, lambda = 3),
C = round(rnorm(1000, mean = -1)),
D = round(rnorm(1000, mean = 0)))
I would like to compute the distances for every possible combination of my columns (AB, AC, AD, BC, BD, CD) at every row of my dataframe.我想在我的数据帧的每一行计算我的列(AB、AC、AD、BC、BD、CD)的每个可能组合的距离。 This would be the equivalent of doing
df$A - df$B
for every combination.这相当于对每个组合执行
df$A - df$B
。
Can we use the dist()
function to compute this efficiently as I have a very large dataset?由于我有一个非常大的数据集,我们可以使用
dist()
函数来有效地计算它吗? I would like to then convert the dist object into a data.frame
to plot the results with ggplot2
.然后我想将 dist 对象转换为
data.frame
以使用ggplot2
绘制结果。 Unless there is a good tidy
version of doing the above.除非有一个很好的
tidy
版本来完成上述操作。
Many Thanks非常感谢
The closest I got was doing the below, but I am not sure to what the column names refer to.我得到的最接近的是执行以下操作,但我不确定列名指的是什么。
d <- apply(as.matrix(df), 1, function(e) as.vector(dist(e)))
t(d)
dist
will compare every value in a vector to every other value in the same vector, so if you are looking to compare columns row-by-row, this is not what you are looking for. dist
会将向量中的每个值与同一向量中的每个其他值进行比较,因此,如果您要逐行比较列,这不是您要查找的内容。
If you just want to calculate the difference between all columns pairwise, you can do:如果您只想成对计算所有列之间的差异,您可以执行以下操作:
df <- cbind(df,
do.call(cbind, lapply(asplit(combn(names(df), 2), 2), function(x) {
setNames(data.frame(df[x[1]] - df[x[2]]), paste(x, collapse = ""))
})))
head(df)
#> A B C D AB AC AD BC BD CD
#> 1 0 1 -2 -1 -1 2 1 3 2 -1
#> 2 1 1 -1 1 0 2 0 2 0 -2
#> 3 3 1 -2 -1 2 5 4 3 2 -1
#> 4 1 3 0 -1 -2 1 2 3 4 1
#> 5 1 3 0 1 -2 1 0 3 2 -1
#> 6 3 3 1 0 0 2 3 2 3 1
Created on 2022-06-14 by the reprex package (v2.0.1)由reprex 包于 2022-06-14 创建 (v2.0.1)
Using base r:使用基数 r:
df_dist <- t(apply(df, 1, dist))
colnames(df_dist) <- apply(combn(names(df), 2), 2, paste0, collapse = "_")
If you really want to use a tidy-approach, you could go with c_across
, but this also removes the names, and is much slower if your data is huge如果您真的想使用整洁的方法,则可以使用
c_across
,但这也会删除名称,并且如果您的数据很大,则速度会慢得多
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