3D PCA -- Can you add jitter to points? Multiple points in one location only show up as one point, and I want to see all points.

[#1]

Hello Community, 

I am using JMP Genomics 10 to make a 3D PCA (Copy Number -> Correlation and Principal Variance Component Analysis). Several points are located in the same spot and show up as one point. However, I would like it to be somehow apparent that there are multiple points there, as I am trying to show how samples in the same group cluster together. I can only tell that one point is representing multiple points if I hover and the labels show up (see image below; apologies for the poor image quality). Note: I am labeling each point according to what Group they fall into (Group 1-4). 

If you have any advice I would greatly appreciate it! Thank you in advance for your time. 

[#2]

It would be much easier if you attached the JMP data table, but understand you may not be permitted to do this.  So her are my thoughts (which I can't try):

1. Often, right clicking on the graph will bring up options (many).  I think if you choose Points, you have the option to Jitter them.

2. Create a column (you could use Recode) that designates the grouping you define and use this column when plotting the data.

[#3 · Accepted solution]

There is a Jitter option under the Red Triangle next to the words Scatterplot 3D, but it only appears when the data type is character, not numeric like PCs in your example.

Basically you have samples that have the same values for the first 3 PCs. You could switch out one of the PCs (like Prin3) for a different PC (like Prin4 if it exists) and that would help separate them, unless they all have the same values for all PCs. That would mean they are identical samples as far as the collected data being used for PVCA. That in itself says either they are redundant, identical, non-informative, the same, or some other similar conclusion. That maybe helpful or not. Depends on the study or experiment.

IF you want to force jitter, you would then have to do the following:

1. Click on View Data button, then select the Prin columns
2. Go to Cols menu and choose Standardized Attributes.
3. Change Data Type from Numeric to Character.
4. The 3D plot will automatically change and the Jitter option will appear in the Red Triangle and automatically be selected

Although not elegant, it does work.

[#4]

@Chris_Kirchberg Thanks for your response! That works! 

Have a great day. 

[#5]

I have attached data tables that hopefully are helpful in answering this question! Thank you for your consideration. 

I use JMP Genomics and the Correlation and Principal Variance Component Analysis function. Below are the settings I changed for each tab -- if not mentioned, then I used the default settings.

General Tab:

• Input SAS Data set = "PCA Groups Data 1". File is attached. 

Experimental Design tab:

• Experimental Design SAS Data Set = "PCA Groups Exp file 1". File is attached.
• Color Variables =Group
• Experimental Factor Variables = Group
• Label Variable = Group 

PCA tab:

• Center rows
• Pearson Correlation 

@statman , thank you for your suggestions!

1) When I right click on the graph area, I don't see "points" as an option or any option that involved jittering. I see the following: Reset, settings..., Hide Lights Border, Wall Color, Background color, Rows, Use Hardware Acceleration, Show ArcBall. Clicking on Settings allows options for changing the size and color of the points but not to jitter them. Is there another way to access the menu you're talking about?

2) I do include an Experimental Design table that defines each group, as required by the JMP Genomics process, and it yields the result I included an image of. So it doesn't help with the jittering issue, unfortunately. 

Thank you all for your consideration.