Tutorial 2: Using CAP#

The CAP class is designed to perform CAPs analyses (on all subjects or group of subjects). It offers the flexibility to analyze data from all subjects or focus on specific groups, compute CAP-specific metrics, and generate visualizations to aid in the interpretation of results.

Performing CAPs on All Subjects#

All information pertaining to CAPs (k-means models, activation vectors/cluster centroids, etc) are stored as attributes in the CAP class and this information is used by all methods in the class. These attributes are accessible via properties. Some properties can also be used as setters.

import numpy as np
from neurocaps.analysis import CAP

# Extracting timseries
parcel_approach = {"Schaefer": {"n_rois": 100, "yeo_networks": 7, "resolution_mm": 2}}

# Simulate data for example
subject_timeseries = {str(x): {f"run-{y}": np.random.rand(100, 100) for y in range(1, 4)} for x in range(1, 11)}

# Initialize CAP class
cap_analysis = CAP(parcel_approach=parcel_approach)

# Get CAPs
cap_analysis.get_caps(
    subject_timeseries=subject_timeseries,
    n_clusters=range(2, 11),
    cluster_selection_method="elbow",
    show_figs=True,
    step=2,
    progress_bar=True,  # Available in versions >= 0.21.5
)

Clustering [GROUP: All Subjects]: 100%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 9/9 [00:00<00:00, 20.38it/s]
2025-03-09 08:20:26,819 neurocaps.analysis.cap [INFO] [GROUP: All Subjects | METHOD: elbow] Optimal cluster size is 5.
../_images/All_Subjects_elbow.png

print can be used to return a string representation of the CAP class.

print(cap_analysis)

Metadata:
================================================
Parcellation Approach                           : Schaefer
Groups                                          : All Subjects
Number of Clusters                              : [2, 3, 4, 5, 6, 7, 8, 9, 10]
Cluster Selection Method                        : elbow
Optimal Number of Clusters                      : {'All Subjects': np.int64(5)}
CPU Cores Used for Clustering (Multiprocessing) : None
User-Specified Runs IDs Used for Clustering     : None
Concatenated Timeseries Bytes                   : 2400184 bytes
Standardized Concatenated Timeseries            : True
Co-Activation Patterns (CAPs)                   : {'All Subjects': 5}
Variance Explained by Clustering                : {'All Subjects': np.float64(0.02448526803307005)}

Performing CAPs on Groups#

cap_analysis = CAP(groups={"A": ["1", "2", "3", "5"], "B": ["4", "6", "7", "8", "9", "10"]})

cap_analysis.get_caps(
    subject_timeseries=subject_timeseries,
    n_clusters=range(2, 21),
    cluster_selection_method="silhouette",
    show_figs=True,
    step=2,
    progress_bar=True,
)

Clustering [GROUP: A]: 100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 19/19 [00:01<00:00, 18.71it/s]
2025-01-31 13:29:54,234 neurocaps.analysis.cap [INFO] [GROUP: A | METHOD: silhouette] Optimal cluster size is 2.
../_images/A_silhouette.png 
Clustering [GROUP: B]: 100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 19/19 [00:01<00:00, 12.48it/s]
2025-01-31 13:29:57,757 neurocaps.analysis.cap [INFO] [GROUP: B | METHOD: silhouette] Optimal cluster size is 2.
../_images/B_silhouette.png

Calculate Metrics#

Note that if standardize was set to True in CAP.get_caps(), then the column (ROI) means and standard deviations computed from the concatenated data used to obtain the CAPs are also used to standardize each subject in the timeseries data inputted into CAP.calculate_metrics(). This ensures proper CAP assignments for each subjects frames.

df_dict = cap_analysis.calculate_metrics(
    subject_timeseries=subject_timeseries,
    return_df=True,
    metrics=["temporal_fraction", "counts", "transition_probability"],
    continuous_runs=True,
    progress_bar=True,
)

print(df_dict["temporal_fraction"])

Computing Metrics for Subjects: 100%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 10/10 [00:00<00:00, 159.78it/s]

Subject_ID

Group

Run

CAP-1

CAP-2

1

A

run-continuous

0.5066666666666667

0.49333333333333335

2

A

run-continuous

0.5333333333333333

0.4666666666666667

3

A

run-continuous

0.6

0.4

5

A

run-continuous

0.54

0.46

4

B

run-continuous

0.41333333333333333

0.5866666666666667

6

B

run-continuous

0.47333333333333333

0.5266666666666666

7

B

run-continuous

0.44

0.56

8

B

run-continuous

0.5

0.5

9

B

run-continuous

0.4866666666666667

0.5133333333333333

10

B

run-continuous

0.46

0.54

Plotting CAPs#

import seaborn as sns

cap_analysis = CAP(parcel_approach=extractor.parcel_approach)

cap_analysis.get_caps(subject_timeseries=subject_timeseries, n_clusters=6)

sns.diverging_palette(145, 300, s=60, as_cmap=True)

palette = sns.diverging_palette(260, 10, s=80, l=55, n=256, as_cmap=True)

kwargs = {
    "subplots": True,
    "fontsize": 14,
    "ncol": 3,
    "sharey": True,
    "tight_layout": False,
    "xlabel_rotation": 0,
    "hspace": 0.3,
    "cmap": palette,
}

cap_analysis.caps2plot(visual_scope="regions", plot_options="outer_product", show_figs=True, **kwargs)
../_images/All_Subjects_CAPs_outer_product_heatmap-regions.png 
cap_analysis.caps2plot(
    visual_scope="nodes", plot_options="heatmap", xticklabels_size=7, yticklabels_size=7, show_figs=True
)
../_images/All_Subjects_CAPs_heatmap-nodes.png

Generate Pearson Correlation Matrix#

cap_analysis.caps2corr(annot=True, cmap="viridis", show_figs=True)
../_images/All_Subjects_CAPs_correlation_matrix.png 
corr_dict = cap_analysis.caps2corr(return_df=True)
print(corr_dict["All Subjects"])

CAP-1

CAP-2

CAP-3

CAP-4

CAP-5

CAP-6

CAP-1

1 (0)***

-0.24 (0.016)*

-0.26 (0.01)*

-0.1 (0.3)

-0.17 (0.087)

-0.17 (0.09)

CAP-2

-0.24 (0.016)*

1 (0)***

-0.11 (0.28)

-0.15 (0.14)

-0.28 (0.0051)**

-0.28 (0.0055)**

CAP-3

-0.26 (0.01)*

-0.11 (0.28)

1 (0)***

-0.3 (0.0021)**

-0.18 (0.075)

-0.19 (0.058)

CAP-4

-0.1 (0.3)

-0.15 (0.14)

-0.3 (0.0021)**

1 (0)***

-0.18 (0.076)

-0.22 (0.028)*

CAP-5

-0.17 (0.087)

-0.28 (0.0051)**

-0.18 (0.075)

-0.18 (0.076)

1 (0)***

-0.17 (0.089)

CAP-6

-0.17 (0.09)

-0.28 (0.0055)**

-0.19 (0.058)

-0.22 (0.028)*

-0.17 (0.089)

1 (0)***

Creating Surface Plots#

from matplotlib.colors import LinearSegmentedColormap

# Create the colormap
colors = [
    "#1bfffe",
    "#00ccff",
    "#0099ff",
    "#0066ff",
    "#0033ff",
    "#c4c4c4",
    "#ff6666",
    "#ff3333",
    "#FF0000",
    "#ffcc00",
    "#FFFF00",
]

custom_cmap = LinearSegmentedColormap.from_list("custom_cold_hot", colors, N=256)

# Apply custom cmap to surface plots
cap_analysis.caps2surf(progress_bar=True, cmap=custom_cmap, size=(500, 100), layout="row")

Generating Surface Plots [GROUP: A]: 100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 2/2 [00:07<00:00,  3.91s/it]
../_images/All_Subjects_CAP-1_surface_plot.png 
Generating Surface Plots [GROUP: B]: 100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 2/2 [00:04<00:00,  2.12s/it]
../_images/All_Subjects_CAP-2_surface_plot.png

Plotting CAPs to Radar#

radialaxis = {
    "showline": True,
    "linewidth": 2,
    "linecolor": "rgba(0, 0, 0, 0.25)",
    "gridcolor": "rgba(0, 0, 0, 0.25)",
    "ticks": "outside",
    "tickfont": {"size": 14, "color": "black"},
    "range": [0, 0.6],
    "tickvals": [0.1, "", "", 0.4, "", "", 0.6],
}

legend = {
    "yanchor": "top",
    "y": 0.99,
    "x": 0.99,
    "title_font_family": "Times New Roman",
    "font": {"size": 12, "color": "black"},
}

colors = {"High Amplitude": "red", "Low Amplitude": "blue"}

kwargs = {
    "radialaxis": radial,
    "fill": "toself",
    "legend": legend,
    "color_discrete_map": colors,
    "height": 400,
    "width": 600,
}

cap_analysis.caps2radar(**kwargs)
../_images/All_Subjects_CAP-1_radar.png ../_images/All_Subjects_CAP-2_radar.png