11.10.1. FATCAT_matplot

../../_images/FATCAT_matplot_main.png

Ready, ready, ready, ready, ready to run. 1

  1. Make sure AFNI and R are installed and configured correctly.

    See installation.

  2. Run @afni_R_package_install -shiny -circos to install necessary R libraries.

  3. Process some data with FATCAT or 3dNetcorr.

  4. Put the output .grid or .netcc datasets in some folder.

Gotta get up to get down. 2

Launch FATCAT matplot from the terminal with:

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

Dataset Selector

All valid datasets in the chosen folder are listed in this drop down selector:

../../_images/FATCAT_matplot_file_picker_edit.png

The selected dataset will be read in and parsed. If there are a lot of regions and statistics, a progress bar will be displayed. The first statistic in the dataset will be automatically loaded and displayed.

Statistic Selector

All statistics in the selected dataset are listed in this drop down selector:

../../_images/FATCAT_matplot_stat_picker.png

The statistics for FATCAT might be FA, bundle length, number of tracks, etc. For 3dNetCorr, they could be Pearson correlation, Fisher Z-score, etc.

ROI Selector

Include/exclude ROIs:

All ROIs selected by default:

Multi-select any combination of ROIs:
../../_images/FATCAT_matplot_roi_select.png
../../_images/FATCAT_matplot_roi_select_some.png

Zoom

Not all ROIs are visible when there are many:

Default shows as many as possible:

Click and drag to zoom in:
../../_images/FATCAT_matplot_unzoomed.png
../../_images/FATCAT_matplot_zoomed.png

Raw Histogram

Before any data manipulation:

Show histogram of the data:

Scroll down:
../../_images/FATCAT_matplot_hist_hide.png
../../_images/FATCAT_matplot_full_hist.png

Triangle

Show or hide the upper or lower triangle of the matrix:

../../_images/FATCAT_matplot_triangle.png

This also hides the diagonal.

Threshold

Threshold the data values in the matrix:

  • Lowpass keeps anything below the selected value.

  • Highpass keeps anything above the selected value.

  • This is automatically filled with suggested values.
../../_images/FATCAT_matplot_thresh.png

  • The histogram will update with the values after thresholding.
../../_images/FATCAT_matplot_thresh_hist.png

Remove Zeros

Only makes sense for some datasets and statistics:

With zeros:

Zeros removed:
../../_images/FATCAT_matplot_with_zeros.png
../../_images/FATCAT_matplot_remove_zeros.png

Clustering

Hierarchical cluster analysis reorders the regions:

No clustering:

Complete linkage with Euclidean distance:
../../_images/FATCAT_matplot_no_clustering.png
../../_images/FATCAT_matplot_clustering.png

Log Files

Download .csv file with the edited matrix and editing parameters:

Save selections and output matrix values:

.csv output with header:
../../_images/FATCAT_matplot_log.png
../../_images/FATCAT_matplot_log_csv.png

Colors

Editing colors:

Defaults to 3 different colors:

Select with color picker:
../../_images/FATCAT_matplot_colors.png
../../_images/FATCAT_matplot_color_picker.png

No edit to min/max leaves data as is:

Histogram is of the actual data:
../../_images/FATCAT_matplot_pre_min_max.png
../../_images/FATCAT_matplot_pre_min_max_hist.png

Editing the min/max changes the data:

Histogram shows edited data:
../../_images/FATCAT_matplot_post_min_max.png
../../_images/FATCAT_matplot_post_min_max_hist.png

  • 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:
../../_images/FATCAT_matplot_min_max_warning.png

Download Heatmap

Heatmap as .png:

Download with dendrogram from clustering:

May take a few seconds to render with many ROIs:
../../_images/FATCAT_matplot_heatmap_png.png
../../_images/o.OME1_000.grid_NT_heatmap.png

  • May want higher DPI for posters or publications.

  • Image size is fixed at 20x20 inches. (post to the message board if you want it variable)

Download Circos

Circos as .png:

Download:

May take a few seconds to render with many ROIs:

Looks better with fewer connections:
../../_images/FATCAT_matplot_circos_png.png
../../_images/o.OME1_000.grid_NT_circos.png
../../_images/REST_corr_rz_circos.png

  • 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

1

Ready to Run by the Dixie Chicks.

2

Fastlove by George Micheal. Original: Brass Construction

3

The Police