Question: Hi all:

I am working with Affymetrix microarray data for my entry to microarray analysis. However, I am trying to see data points distribution within labeled groups in the 3D plot, because I want to see how similar each group of data points in 3D space. To do so, I used `scatterplot3d` package from CRAN to get 3D to scatter plot, didn't get the correct plot for my data.

So my guess could be the first cluster my data points that belong to different labeled groups then render them in 3D space. Here is my reproducible data that simulated from the [actual dataset:][1]

**reproducible data**

> dput(head(phenDat,30))
structure(list(SampleID = c("Tarca_001_P1A01", "Tarca_013_P1B01",
"Tarca_025_P1C01", "Tarca_037_P1D01", "Tarca_049_P1E01", "Tarca_061_P1F01",
"Tarca_051_P1E03", "Tarca_063_P1F03", "Tarca_075_P1G03", "Tarca_087_P1H03",
"Tarca_004_P1A04", "Tarca_064_P1F04", "Tarca_076_P1G04", "Tarca_088_P1H04",
"Tarca_005_P1A05", "Tarca_017_P1B05", "Tarca_054_P1E06", "Tarca_066_P1F06",
"Tarca_078_P1G06", "Tarca_090_P1H06", "Tarca_007_P1A07", "Tarca_019_P1B07",
"Tarca_031_P1C07", "Tarca_079_P1G07", "Tarca_091_P1H07", "Tarca_008_P1A08",
"Tarca_020_P1B08", "Tarca_022_P1B10", "Tarca_034_P1C10", "Tarca_046_P1D10"
), GA = c(11, 15.3, 21.7, 26.7, 31.3, 32.1, 19.7, 23.6, 27.6,
30.6, 32.6, 12.6, 18.6, 25.6, 30.6, 36.4, 24.9, 28.9, 36.6, 19.9,
26.1, 30.1, 36.7, 13.6, 17.6, 22.6, 24.7, 13.3, 19.7, 24.7),
Batch = c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L), Set = c("PRB_HTA", "PRB_HTA", "PRB_HTA", "PRB_HTA",
"PRB_HTA", "PRB_HTA", "PRB_HTA", "PRB_HTA", "PRB_HTA", "PRB_HTA",
"PRB_HTA", "PRB_HTA", "PRB_HTA", "PRB_HTA", "PRB_HTA", "PRB_HTA",
"PRB_HTA", "PRB_HTA", "PRB_HTA", "PRB_HTA", "PRB_HTA", "PRB_HTA",
"PRB_HTA", "PRB_HTA", "PRB_HTA", "PRB_HTA", "PRB_HTA", "PRB_HTA",
"PRB_HTA", "PRB_HTA"), Train = c(1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L), Platform = c("HTA20",
"HTA20", "HTA20", "HTA20", "HTA20", "HTA20", "HTA20", "HTA20",
"HTA20", "HTA20", "HTA20", "HTA20", "HTA20", "HTA20", "HTA20",
"HTA20", "HTA20", "HTA20", "HTA20", "HTA20", "HTA20", "HTA20",
"HTA20", "HTA20", "HTA20", "HTA20", "HTA20", "HTA20", "HTA20",
"HTA20")), row.names = c(NA, 30L), class = "data.frame")

**my attempt**:

hclustfunc <- function(x) hclust(x, method="complete")
distfunc <- function(x) as.dist((1-cor(t(x)))/2)
d <- distfunc(persons_df)
fit <- hclustfunc(d)

but seems I need to group data points that belong to each individual groups (for instance, in the batch column, there are 4 different batches), then use either PCA or clustering or k-means to measure the distance then render them in 3D space with 3D scatter plot. But so far my attempts didn't bring up my expected plot.

basically, I want to see data points (a.k.a, rows) that belong to different batch (or group), wanted to color them by some 'group' attribute. I just want to see how data points are similar to each other if we grouped them by different age categories (I used `findInterval(persons_df$ages, c(10,20,30,40,50))`), different batch, and different platform

I am thinking to use kmeans, PCA, other methods can give me different components that can be visualized in 3D plot, but this is not very intuitive to me how to do it in R?

**desired plot**

I want to get 3D plot something like this:

can anyone point me out how can I possibly to make this happen? any way to get cluster my data and visualize it in 3D plot in R? Any thoughts? Thanks

[1]: https://jumpshare.com/v/eZhYBHZm1MGfFDMx7MXq

Answer: First, read the docs of the functions you're using. hclust() does hierarchical clustering which means it produces a tree, not individual clusters. To get these, you need to cut the tree (check ?cutree).
Second, you don't need to wrap a function in another function if you're not somehow modifying it, i.e. you can just do

d <- as.dist((1-cor(t(x)))/2)
tree <- hclust(d, method="complete")
This makes the code clearer.

Once you have a vector of cluster memberships and a vector of associated colors, you can use them to assign colors. For a 3D scatter plot, I use something like this:

library(rgl)
library(car)
scatter3d(x = PC1, y = PC2, z = PC3, surface = FALSE, groups = as.factor(clusters), surface.col = cluster.colors, col = cluster.colors, xlab="PC1",ylab="PC2",zlab="PC3")

To recap:

- Read the docs of the functions you intend to use
- Cluster your data to obtain a vector of cluster memberships
- Get a vector of colors you want to associate with each cluster
- Plot using the appropriate syntax for the plotting function of your choice.