# Visualizing geomorph2slicermorph2 output in 3DSlicer: PCA plot differences?

**URL:** <https://discourse.slicer.org/t/visualizing-geomorph2slicermorph2-output-in-3dslicer-pca-plot-differences/45866>\
**Category:** Support\
**Created:** [January 22, 2026, 3:41pm UTC](https://discourse.slicer.org/t/visualizing-geomorph2slicermorph2-output-in-3dslicer-pca-plot-differences/45866 "2026-01-22T15:41:54Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![katrust](https://avatars.discourse-cdn.com/v4/letter/k/d2c977/32.png) [@katrust](https://discourse.slicer.org/u/katrust)\
**Post date:** [January 22, 2026, 3:41pm UTC](https://discourse.slicer.org/t/visualizing-geomorph2slicermorph2-output-in-3dslicer-pca-plot-differences/45866/1 "2026-01-22T15:41:54Z")

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I am concerned about some differences I am seeing in my PCA scatterplot in 3DSlicer after having produced GPA and PCA results to slide semi-LMs in the geomorph R package.

As a very coarse way to sanity checking myself, I uploaded my geomorph output to 3DSlicer to better visualize which specimens fall where in the morphospace (a very convenient feature in SlicerMorph). As you can see in the Geomorph R PCA plot, a datapoint with a factor of stage “2” and colored pink is positioned in the lower right quadrant at the intersection of .02 on PC1 and close to -.06 on PC2.

When I uploaded this geomorph output into 3Dslicer to see which specimen this is, I went to search for that specific data point and I can’t seem to locate it in the morphospace where my Geomorph R plotted it along PC1 and PC2.

Now, as I compare the plots, I am concerned about the overall differences in these scatterplots. Of course scaling differences between plots can alter the visualization of the data, but as I compare the plots, I don’t think that’s the case. Am I missing something here?

 ![Screenshot 2026-01-20 at 1.48.26 PM](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/2/5/252f08b09aad0e38f82a8716ce0e31279a8f9a36.png)

 ![Screenshot 2026-01-20 at 1.51.59 PM](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/5/9/5999f77817291ebac63f01614308116b430ad5df.png)

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**Author:** ![muratmaga](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/muratmaga/32/3622_2.png) [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Post date:** [January 22, 2026, 4:37pm UTC](https://discourse.slicer.org/t/visualizing-geomorph2slicermorph2-output-in-3dslicer-pca-plot-differences/45866/2 "2026-01-22T16:37:51Z")

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As far as I can tell the sign of PC2 has changes between those two plots. PC signs are arbitrary, so I wouldn’t be concerned about those. But if you want to be sure, you can just run a correlation of the values between geomorph and slicermorph. I suspect it will come as -1.