@FATCAT_matplot_shiny Error

AFNI Message Board
1

Hi Afni experts,

i try this command @FATCAT_matplot_shiny but i’ve an error:

Loading required package: tools
Error in basename(file.list2) : a character vector argument expected
Calls: … sourceUTF8 → eval → eval → …stacktraceon… → basename
Execution halted

the netcc file inside the directory contain this:

4 # Number of network ROIs

2 # Number of netcc matrices

WITH_ROI_LABELS

LFovea_LO LLO LMT RV3A
1 2 3 4

CC

  1.0000	      0.2271	     -0.1172	     -0.2258
  0.2271	      1.0000	      0.3991	      0.1092
 -0.1172	      0.3991	      1.0000	      0.3055
 -0.2258	      0.1092	      0.3055	      1.0000

FZ

  4.0000	      0.2312	     -0.1177	     -0.2297
  0.2312	      4.0000	      0.4226	      0.1096
 -0.1177	      0.4226	      4.0000	      0.3156
 -0.2297	      0.1096	      0.3156	      4.0000

thanks

2

Hi,

Is there only one file in the folder?
And what is the name of the file?

Thanks, Justin

3

Hi,
below the list of file:

FCN004_3dNetCorr_CorrMat_000.netcc
FCN004_3dNetCorr_CorrMat_000.niml.dset
FCN004_3dNetCorr_CorrMat_000.roidat

the files are created by 3dNetCorr command.

thanks,
Piero

4

Hi,
Thanks for finding that bug for me!
It is fixed and will be in the next version update.

But if you need it now, you can download a fix here:
http://afni.nimh.nih.gov/pub/dist/data/shiny_temp/global.R

You should right click the link and “Save As”.
Then use that “global.R” to replace the previous one in your abin folder (or wherever you put afni)
/shiny/FATCAT_matplot_shiny/global.R
( should be replaced by the path to your afni installation)

Let me know if that fixes it for you.

thanks, Justin

5

thank you, now work! :slight_smile:

6

Great!

If you make some pretty graphs that you can share, can you post them here?

7

Ok asap.
Is possible have some help documentation about right menu (for example what does it mean “cluster linkage”?)

There is a little graphic problem i’ve 169 ROI with each label but when display the matrix i don’t see all labels, i suppose because there are so many. It’s possible change size of label?

thanks

Piero

8

Hi,
The cluster linkage methods are what is used to calculate hierarchical clustering.
It basically rearranges the data based on dissimilarities of the regions.
The descriptions of the methods are here:
https://stat.ethz.ch/R-manual/R-devel/library/stats/html/hclust.html
There are also a links to the descriptions in the shiny app below the drop down selectors.

For the many ROI problems, you can zoom in on the interactive matrix by clicking and dragging.
But the best way to see everything is to download a png version of the heatmap.
The menu on the left has a “Heatmap PNG”.
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/tutorials/FATCAT_matplot/FATCAT_matplot.html#download-heatmap
The PNG is very large so you should be able to see every ROI label.

I hope that helps some.

Thanks, Justin