R中的3D阵列聚类 [英] clustering 3D array in R

问题描述

我正在尝试对阵列中的3D数据进行聚类。它实际上是来自3D图像的信息，因此此数组代表具有x，y，z值的单个图像。我想知道什么体素倾向于与什么聚类。数组看起来像这样。

I'm trying to cluster 3D data that I have in an array. It's actually information from a 3D image so this array represents a single image with x,y,z values. I would like to know what voxel tends to cluster with what. The array looks like this.

 dim(x)
[1] 34 34 34  1

我该怎么办？我试过只用scatterplot3d进行绘图，但是没有用。

How can I go about this? I tried just plotting with scatterplot3d but it did not work.

推荐答案

因此，这是对群集的尝试。

So this is an attempt at clustering. You really should provide data if you want a better answer.

library(reshape2)   # for melt(...)
library(rgl)        # for plot3d(...)

set.seed(1)         # to create reproducible sample

# 3D matrix, values clustered around -2 and +2
m      <- c(rnorm(500,-2),rnorm(500,+2))
dim(m) <- c(10,10,10) 
v      <- melt(m, varnames=c("x","y","z"))  # 4 columns: x, y, z, value
# interactive 3D plot, coloring based on value
plot3d(v$x,v$y,v$z, col=1+round(v$value-min(v$value)),size=5)
# identify clusters
v      <- scale(v)                          # need to scale or clustering will fail
v      <- data.frame(v)                     # need data frame for later
d  <- dist(v)                               # distance matrix
km <- kmeans(d,centers=2)                   # kmeans clustering, 2 clusters
v$clust <- km$cluster                       # identify clusters
# plot the clusters
plot(z[1:4],col=v$clust)                    # scatterplot matrix
plot3d(v$x,v$y,v$z, col=v$clust,size=5)     # 3D plot, colors based in cluster

主要思想是将3D矩阵重塑为长格式，其中包含x，y，z和实际矩阵值的列。因此，现在x，y和z包含位置信息（此处为索引值1:10）。您需要对其进行缩放，以使值列和索引列的缩放比例相同，否则聚类会给您带来误导的结果。

The main idea is to reshape your 3D matrix into "long" format with columns for x, y, z, and the actual matrix values. So now x, y, and z contain the positional information (here, the index values 1:10). You need to scale this so the value column and the index columns are on the same scale, otherwise clustering will give you misleading results.

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