R help - Aug 2016 - question about cleaning up data labels on a plot3d plot

Hello,

I am rather unfamiliar with R but need a 3D plot for something I am working on.

I was able to generate a plot with the following,

library(rgl)
setwd("G:/shared_data/R_projects/3D_plot")
df <- read.table("R_input_3D_PCA-3_RI9_60.txt", header = TRUE)
plot3d(df$PCA_Axis1, df$PCA_Axis2, df$PCA_Axis3, col="blue", size=10)

My data is tab delimited and looks like,

num  PCA_Axis1   PCA_Axis2   PCA_Axis3
11   -0.672164   -0.83449    -1.06511
12   -1.23009    1.57928     -0.066808
42   2.80029     0.533236    -0.197187
60   2.25999     -0.233224   -0.00267827
67   1.82422     -0.840649   0.156681

There are a total of 60 rows.

Adding,

text3d(df, text=df$num)

displays my index value on the plot, but the numbers are very hard to read. It
looks
like the the labels are behind the points. Is there any way to clean this up
some? I
guess I could color the points white so I only see the numbers.

I also have 2 or three different sub groups within the data. Is there any way to
have
these different groups appear in different colors? I could create multiple 
data.frames if that would help. I am not sure you can display data from multiple
frames on the same plot.

Suggestions would be appreciated,

LMH

Sure, you can do any of that in R.

You might benefit from reading some introductory material so you
understand at least graphical parameters and subsetting, but here's
some sample code with fake data that does what you're asking.

library(rgl)
x <- sort(rnorm(10))
y <- rnorm(10)
z <- rnorm(10) + atan2(x, y)

# version one: text only

plot3d(x, y, z, type="n")
text3d(x, y, z, text=letters[1:10], cex=2)


# version two: colored symbols
data.groups <- sample(1:3, size=10, replace=TRUE)
data.colors <- c("red", "purple", "blue")

plot3d(x, y, z, size=8, col=data.colors[data.groups])


Sarah

On Wed, Aug 24, 2016 at 1:57 AM, LMH <lmh_users-groups at molconn.com>
wrote:
> Hello,
>
> I am rather unfamiliar with R but need a 3D plot for something I am working
> on.
>
> I was able to generate a plot with the following,
>
> library(rgl)
> setwd("G:/shared_data/R_projects/3D_plot")
> df <- read.table("R_input_3D_PCA-3_RI9_60.txt", header = TRUE)
> plot3d(df$PCA_Axis1, df$PCA_Axis2, df$PCA_Axis3, col="blue",
size=10)
>
> My data is tab delimited and looks like,
>
> num  PCA_Axis1   PCA_Axis2   PCA_Axis3
> 11   -0.672164   -0.83449    -1.06511
> 12   -1.23009    1.57928     -0.066808
> 42   2.80029     0.533236    -0.197187
> 60   2.25999     -0.233224   -0.00267827
> 67   1.82422     -0.840649   0.156681
>
> There are a total of 60 rows.
>
> Adding,
>
> text3d(df, text=df$num)
>
> displays my index value on the plot, but the numbers are very hard to read.
> It looks like the the labels are behind the points. Is there any way to
> clean this up some? I guess I could color the points white so I only see
the
> numbers.
>
> I also have 2 or three different sub groups within the data. Is there any
> way to have these different groups appear in different colors? I could
> create multiple data.frames if that would help. I am not sure you can
> display data from multiple frames on the same plot.
>
> Suggestions would be appreciated,
>
> LMH
>

Sarah Goslee wrote:
> text3d(x, y, z, text=letters[1:10], cex=2
Thank you for the help. Is there a way to remove the text from the plot as well.

I am finding it difficult to see what I am looking for with the text in the way.
It
would be useful to be able to identify a point and then clear the text. Can that
be
done while still maintaining the orientation of the plot?

LMH