SpaceMap

API Reference

Note

This plot can be saved in an interactive form, see Saving plots

Spatially map a categorical variable onto a projection of a Sample’s image sequence

Note

Image produced from the following dataset: Garner, Aleena (2014): In vivo calcium imaging of layer 4 cells in the mouse using sinusoidal grating stimuli. CRCNS.org. http://dx.doi.org/10.6080/K0C8276G

Video Tutorial

This shows how you can view a space map that shows the tuning of cells. The Space map plot itself is shows after 3:38.

Controls

Parameter	Description
Patch labels	Categorical column to use for the patch labels
Image Colormap	Colormap for the image
Patches Colormap	Colormap for the patches
Projection	Show the image as a “Max” or “Standard Deviation” projection
Fill Patches	Fill the patches
Line width	Line width of the patches
Alpha	Alpha level of the patches
Samples	Click on the sample to plot
Save	Save the plot data and state in an interactive form
Load	Load a plot that has been saved as a “.ptrn” file.

Console

See also

API Reference

Namespace

reference	Description
this	The SpaceMapWidget instance, i.e. the entire widget
this.transmission	Current input Transmission
get_plot()	Returns the plot area
get_plot().fig	Returns the matplotlib Figure instance
get_plot().ax	Returns the Axes for the current plot matplotlib Axes

Examples

Export

See also

matplotlib API for: Figure.savefig, Figure.set_size_inches, Figure.get_size_inches

# Desired size (width, height)
size = (6,5)

# Get the figure
fig = get_plot().fig

# original size to reset the figure after we save it
orig_size = fig.get_size_inches()

#Set the desired size
fig.set_size_inches(size)

# Save the figure as a png file with 600 dpi
fig.savefig('/share/data/temp/kushal/spacemap.png', dpi=600, bbox_inches='tight', pad_inches=0)

# Reset to original size and draw
fig.set_size_inches(orig_size)
get_plot().draw()

Note

The entire plot area might go gray after the figure is reset to the original size. I think this is a Qt-matplotlib issue. Just resize the window a bit and the plot will be visible again!

Legend Title

See also

matplotlib API for matplotlib.axes.Axes.get_legend

get_plot().ax.get_legend().set_title('New Title')
get_plot().draw()

Hide Axis Borders

See also

matplotlib API for matplotlib.axes.Axes.axis

get_plot().ax.axis('off')
get_plot().draw()