Plotting

sails.plotting.root_plot(rts, ax=None, figargs={}, plotargs={})[source]

Plot a set of roots (complex numbers).

Parameters:
  • rts (ndarray_like) – Roots to plot
  • ax (matplotlib axes handle) – Optional Axes on which to place plot. (Default value = None)
  • figargs (dict) – extra arguments to pass to plt.figure (Default value = dict())
  • plotargs (dict) – extra arguments to pass to plt.plot (Default value = dict())
Returns:

Axes object on which plot was drawn

Return type:

Axes

sails.plotting.plot_vector(metric, x_vect, y_vect=None, x_label=None, y_label=None, title=None, labels=None, line_labels=None, F=None, cmap=<matplotlib.colors.LinearSegmentedColormap object>, triangle=None, diag=False, thresh=None, two_tail_thresh=False, font_size=10, use_latex=False)[source]

Function for plotting frequency domain connectivity at a single time-point.

Parameters:
  • metric (ndarray) – matrix containing connectivity values [nsignals x signals x frequencies x participants] in which the first dimension refers to source nodes and the second dimension refers to target nodes
  • x_vect (ndarray) – vector of frequencies to label the x axis
  • y_vect (ndarrat) – vector containing the values for the y-axis
  • x_label (string [optional]) – label for the x axis (Default value = None)
  • y_label (string [optional]) – label for the y axis (Default value = None)
  • title (string [optional]) – title for the figure (Default value = None)
  • labels (list) – list of node labels for columns and vectors (Default value = None)
  • line_labels (list) – list of labels for each separate line (participant dimension in metric) (Default value = None)
  • F (figurehandle [optional]) – handle of existing figure to plot within (Default value = None)
  • triangle (string [optional]) – string to indicate whether only the ‘upper’ or ‘lower’ triangle of the matrix should be plotted (Default value = None)
  • diag (bool [optional]) – flag to indicate whether the diagonal elements should be plotted (Default value = False)
  • thresh (ndarray [optional]) – matrix containing thresholds to be plotted alongside connectivity values [nsignals x nsignals x frequencies] (Default value = None)
  • two_tailed_thresh (bool [optional]) – flag to indicate whether both signs (+/-) of the threshold should be plotted
  • font_size (int [optional]) – override the default font size
  • use_latex (bool) – Flag to indicate whether to render text in latex (Default value = False)
Returns:

Figure handle containing the plot

Return type:

matplotlib figure handle

sails.plotting.plot_matrix(metric, x_vect, y_vect, x_label=None, y_label=None, z_vect=None, title=None, labels=None, F=None, vlines=None, cmap=<matplotlib.colors.LinearSegmentedColormap object>, font_size=8, use_latex=False, diag=True)[source]

Function for plotting frequency domain connectivity over many time points

Parameters:
  • metric (ndarray) – matrix containing connectivity values [nsignals x signals x frequencies x participants] in which the first dimension refers to source nodes and the second dimension refers to target nodes
  • x_vect (1d array) – vector of frequencies to label the x axis
  • y_vect (1d array [optional]) – vector containing the values for the y-axis
  • z_vect (1d array [optional]) – vector containing values for the colour scale (Default value = None)
  • x_label (string [optional]) – label for the x axis (Default value = None)
  • y_label (string [optional]) – label for the y axis (Default value = None)
  • title (string [optional]) – title for the figure (Default value = None)
  • labels (list) – list of node labels for columns and vectors (Default value = None)
  • F (figurehandle [optional]) – handle of existing figure to plot within (Default value = None)
  • vlines (list) – List of x-axis values to plot a dashed vertical line (Default value = None)
  • cmap (matplotlib colormap [optional]) – matplotlib.cm.<colormapname> to use for colourscale (redundant for plot vector??) (Default value = plt.cm.jet)
  • font_size (int [optional]) – override the default font size
  • use_latex (bool) – Flag indicating whether to render text in latex (Default value = False)
  • diag (bool) – Flag indicating whether to plot the diagonal subplots (Default value = True)
Returns:

Figure handle containing the plot

Return type:

matplotlib figure handle

class sails.circular_plots.CircosHandler[source]

Handler for producing plots using the Circos tool.

Note that if you are creating plots for publication using Circos, you should cite the relevant publication: [Krzywinski2009].

class sails.circular_plots.CircosGroup(name, c_idx=0, n_idx=0, circoscolour='unknown', rgbcolour=None, netmatreverse=False)[source]