11.10.1. FATCAT_matplot¶

Ready, ready, ready, ready, ready to run. 1¶
- Make sure AFNI and R are installed and configured correctly.
Run
@afni_R_package_install -shiny -circos
to install necessary R libraries.Put the output .grid or .netcc datasets in some folder.
Gotta get up to get down. 2¶
FATCAT_matplot ~/my_Netcc_files
With “~/my_Netcc_files” being some folder with .netcc or .grid files. This will open your default web browser and read all valid datasets in “~/my_Netcc_files”.
FATCAT_matplot can also read non FATCAT or 3dnetcorr formatted datasets if they are in the following format:
The data must be a symmetrical square matrix.
There must be row and column names that match.
The row and column names must begin with a letter.
The first cell (upper left) must be empty.
The data needs to be saved as a tab or comma separated file.
The file extension needs to be one of the following: csv, tsv, dat, or 1d.
There can be NO other header information or comments.
So it should look like this:
roi1 |
roi2 |
roi3 |
roi4 |
|
roi1 |
1.0 |
0.2 |
0.3 |
0.4 |
roi2 |
0.2 |
1.0 |
0.5 |
0.6 |
roi3 |
0.3 |
0.5 |
1.0 |
0.7 |
roi4 |
0.4 |
0.6 |
0.7 |
1.0 |
The statistic selector will default to “none” because there is no information as to what the data represents.
Walking in your footsteps. 3¶
Clustering¶
Hierarchical cluster analysis reorders the regions:
No clustering: |
Complete linkage with Euclidean distance: |
Cluster linkage and distance method details are at the links below the drop down selectors.
Colors¶
Editing colors:
Defaults to 3 different colors: |
Select with color picker: |
No edit to min/max leaves data as is: |
Histogram is of the actual data: |
Editing the min/max changes the data: |
Histogram shows edited data: |
Changes the color bar range by changing the data.
Any value below the chosen minimum will be set to the chosen minimum.
Any value above the chosen maximum will be set to the chosen maximum.
In this example, any values > 200 are now changed to 200.
This will also effect the log output: |
Download Circos¶
Circos as .png:
Download: |
May take a few seconds to render with many ROIs: |
Looks better with fewer connections: |
ROI labels with many characters may need a larger image size.
The color picker alpha slider works for the circos plots transparency.
Clustering will reorder the ROIs around the circle.
For a custom order around the circle, the input data should be reordered.
Footnotes