API
Full list of keyword arguments
Here is the full list of keyword arguments (otherwise called KWARGS) that can be used along with netplotbrain.plot. Below they are split up in the following sections
- Node keyword arguments - modify the nodes.
- Edge keyword arguments - modify the edges.
- Template keyword arguments - modify the template.
- Highlighting keyword arguments - modify the highlighting.
- Connectivity matrix keyword arguments - modify the connectivity matrix.
- Template keyword arguments - modify the template.
- Legend keyword arguments - modify the figure legend.
- Arrow keyword arguments - modify the direction arrows.
- Figure keyword arguments - configure the figure as a whole.
- GIF keyword arguments - when exporting as a gif.
- Text keyword arguments - text related variables.
- Profile keyword arguments - setting a style profile for all keyword arguments.
Node keyword arguments
| Argument |
Type |
Description |
| nodes_df |
pd.DataFrame |
Allows for passing additional edge information if nodes is nifti file or templateflow atlas dictionary. Behaves like nodes when input is dataframe. |
| node_cmap |
str |
Matplotlib colormap for node coloring when node_color points to a dataframe. |
| node_color |
matplotlib coloring |
Can be string (default 'black') that points to either a matplotlib color or a column in nodes or nodes_df. Alternatively a list of 3D/4D colors for each node. |
| node_type |
str |
Can be 'spheres', 'circles', or (if nodes is a nifti image) 'parcels'. |
| node_alpha |
float |
Specify the transparency of the nodes |
| node_columnnames |
list |
Node column names in node dataframe. 'auto' entails the columns are ['x', 'y', 'z'] (specifying coordinates) |
| node_sizevminvmax |
str, list |
Scaling alternatives if node_size is given. Alternatives: 'absolute' (default) 'minmax', or 2-tuple list of [min, max]. If minmax, node sizes are scaled between (0 and 1) * node_scale. If absolute, then the default values are used. Absolute can lead to problems with, for example, negative values. |
| node_colorvminvmax |
str, list |
Scales continuous colormap between certain values. Alternatives: 'minmax' (default), 'absmax', , or 2-tuple list of [min, max]. If minmax, colorbar starts at the smallest value to largest value. If absmax, then colorbar goes from -abs(max(value)) to abs(max(value)), ensuring 0 is in the middle. |
EDGE keyword arguments
| Argument |
Type |
Description |
| edges_df |
pd.DataFrame |
Allows for passing additional edge information if edges is np.array. Behaves like edges when input is dataframe. |
| edge_cmap |
str |
Matplotlib colormap for node coloring when node_color points to a dataframe. |
| edge_alpha |
float |
Transparency of edges (default: 1). |
| edgecolumnames |
list |
Edge columns names in edge dataframe. Default is i and j (specifying nodes). |
| edge_color |
matplotlib coloring |
Can be string (default 'black') or list of 3D/4D colors for each edge. Can also be a dictionary with keys positive and negative to denote two different colors for positive and negative edges. |
| edge_weights |
str |
String that specifies column in edge dataframe that contains weights. If numpy array is edge input, can be True (default) to specify edge weights. |
| edge_highlightbehaviour |
str |
Alternatives "both" or "any" or None. Governs edge dimming when highlight_nodes is on. If both, then highlights only edges between highlighted nodes. If any, then only edges connecting any of the nodes are highlighted. |
| edge_widthscale |
int, float |
Scale the width of all edges by a factor (default: 1). |
| edge_thresholddirection |
str |
can be "absabove", "above" (or ">"), "below" (or "<") to indicate thresholding behaviour. If absabove, then the thresholding behaviour is np.abs(edges) > edge_threshold. |
| edge_threshold |
float |
Edgeweight value to threshold edges. |
| edge_colorvminvmax |
str, list |
Scales colormap between certain values. Alternatives: 'minmax' (default), 'absmax', or 2-tuple list of [min, max]. If minmax, colorbar starts at the smallest value to largest value. If absmax, then colorbar goes from -abs(max(value)) to abs(max(value)), ensuring 0 is in the middle. |
TEMPLATE keyword arguments
| Argument |
Type |
Description |
| tempalte |
str, dict or nibabel nifti |
The background template. If str: path to nifti image, or templateflow template name (see templateflow.org) in order to automatically download T1 template. If dict, specify keyword - value pairs for templateflow.api.get(). If specifying templateflow string, and there are multiple cohorts (e.g. MNIInfant) add "_cohort-X" to the string. For example, for MNIInfant, cohort 3, write: "MNIInfant_cohort-3". |
| template_alpha |
float |
Opacity of template voxels. |
| template_color |
str |
If template_style=='surface' or 'filled', the color of template voxels |
| templateedge_threshold |
float |
If template_style=='cloudy', can tweak the edges detection threshold. (Default: 0.7) |
| template_style |
str |
can be 'surface': (a surface is rendered from the template), 'glass': a semi-transparanet brain is generated from the template. 'filled': plot all voxels, 'cloudy': cloudy (cloudy scatter edges outline the figure) |
| template_voxelsize |
int |
Resize voxels this size. Larger voxels = quicker. (Default: 2) |
| surface_detection |
float |
The value used to detect the surface boundary (see argument level in marching_cubes). Some default choices are made for various templates |
| surface_resolution |
int |
If template_style=='surface' controls the size of the triangles used in the surface reconstruction. (Default: 2). |
| template_glass_compactness |
float |
Default 0.3. Compactness argument for skimage.segmentation.slic for segementation. Going lower will increase the detail. >1 will break the figure. |
| temlate_glass_nsegments |
int |
n_segments argument for skimage.segementations.slic. Approx number of segments. 3 seems to work well. Increase if not enough detail, reduce if too much detail. |
| template_glass_maxalpha |
float |
Default is 0.01. To make the smokey effect the alpha is relative to template intensity value This value sets the alpha scalar factor. The value will be the largest possible alpha value, where all other values scale between 0 and template_glass_max_alpha. |
HIGHLIGHTING keyword arguments
highlight_level | float | Intensity of the highlighting (opposite of alpha). Controls both nods and edges together. Value between 0 and 1, if 1, non-highlighted nodes are fully transparent. If 0, non-highlighted nodes are same alpha level as highlighted nodes. Default 0.85.
See also node_highlight and edge_highlight keyword arguments.
Connectviity matrix keyword arguments
| Argument |
Type |
Description |
| cm_border |
bool |
If true prints a border around the connectivity matrix. Default True. |
| cm_bordercolor |
str |
Matplotlib color for border around connectivity matrix. Default gray. |
| cm_borderwidth |
float |
Width of border around connectivity matrix. Default 0.5. |
| cm_boundary |
str |
Can be "auto" (default) or None. Plots a boundrary around communities in connectivity matrix. Auto behaviour defaults to node_color if specified. |
| cm_boundarywidth |
float |
Width of boundary around communities in connectivity matrix. Default 2. |
| cm_order |
Str |
Specify which variable to group and order nodes in connectivity matrix by. Default is "auto". Auto entails that if node_color is a column in the data and if cm_order is unspecified use node_color column. Otherwise if None will plot in list order. |
| cm_rotate |
Bool |
If True, rotates the connectivity matrix 45 degrees. Default True. |
| cm_vmin |
float |
Minimum value for connectivity matrix colormap. Default -1. |
| cm_vmax |
float |
Maximum value for connectivity matrix colormap. Default 1. |
LEGENDkeyword arguments
| Argument |
Type |
Description |
| legend_tick_fontsize |
str, int |
Matplotlib fontsize for title in figure legends |
| legend_title_fontsize |
str, int |
Matplotlib fontsize for ticks in figure legends |
| node_colorlegend |
Bool |
If the colorlegend is plotted or not. Default True. |
| node_sizelegend |
Bool |
If the sizelegend is plotted or not. Default True. |
| node_colorlegendstyle |
str |
Alternatives: auto (default), discrete, continuous. If the color legend should show the entire colormap or discrete colors. If auto, plots discrete if less than 8 unique values are detected. |
| showlegend |
bool, list |
If size or colour have been set, generates a legend for that property at bottom of figure. If True, plots all the legends that can be plotted. If list, can contain 'node_size' and 'node_color' to plot those in the legend. |
| legend_span |
list |
Range of subplot columns for the legend to span. |
ARROW keyword arguments
| Argument |
Type |
Description |
| arrowaxis |
list or str |
Adds axis arrows onto plot. Alternatives are: LR, AP, SI, 'all' |
| arrowlength |
int, float |
Length of arrow |
| arroworigin |
list |
x,y,z coordinates of arrowaxis. Note 0,0,0 is bottom left. |
| Argument |
Type |
Description |
| ax |
matplotlib 3D ax |
fig = plt.figure(). ax = fig.add_subplot(111, projection='3d'). netplotbrain.plot(ax, ...) |
| fig |
matplotlib figure |
|
| savename |
str |
Save path for figure. If string ends with .png or .svg it will one save this figure. if the path ends with anything else, it will save both a .png and .svg figure. Default: None and nothing is saved. |
| figdpi |
int |
300 Default. Resolution of figure when saving png files. |
HEMISPHERE keyword arguments
| Argument |
Type |
Description |
| hemisphere |
string, list |
If string, can be left or right to specify single hemisphere to include. If list, should match the size of views and contain strings to specify hemisphere shown in subplots. Can be abbreviated to "L", "R" and ("both" or empty string possible if both hemisphere plotted). Between hemisphere edges are deleted. |
GIF keyword arguments
| Argument |
Type |
Description |
| gif |
bool |
If true, saves views as a gif. |
| gif_duration |
int |
Gif duration in milliseconds |
| gif_loop |
int |
How many times to loop figure. 0 (default) entails infinite loop. |
TEXT keyword arguments
| Argument |
Type |
Description |
| font |
str |
font for all text in figure. |
| fontcolor |
str, list, tuple |
font color for all text in figure |
| title_fontsize |
str |
Size of title font (default: medium). See matplotlib "fontsize" |
| titleloc |
str, |
Location of title (default: center). See matplotlib "loc" |
| title_weight |
str |
Font weight of title (default: regular). See matplotlib "fontweight" |
Other keyword arguments
| Argument |
Type |
Description |
| seed |
int |
Pseudorandom integer seed for reproducibility for certain functions (e.g. spring_layout) |
| profile |
str |
path or name of file in netplotbrain/profiles/.json, specifies default keyword arguments. Default points to netplotbrain/profiles/default.json |