Adjust spacing between plots arranged using `gridplot`

I effectively want to duplicate the selection_histogram.py dashboard without the large gaps between the side histograms and the center plot. If I arrange two plots using row or column there is much less space than gridplot but I can’t actually figure out how to control that value.

I saw in a similar question (remove all spacing between plots in a grid plot) the recommendation to set p.min_border = 0 for each of the different plots. I tried this and perhaps there was a small change but not much. I did not try using a yaml file.

Is there a way to do this without a yaml file?

Putting things in a grid plot aligns the plot frames. You will have to get rid of the right axis on the bottom histogram (e.g. move it to the left side) and the bottom axis on the right histogram (e.g. move it to the top). Those are what are causing the top left plot to pad.

Edit: I suppose you could also move the axes in to the center areas of the respective plots, too.

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That makes sense, thank you! Once I moved the axes to the edges of the grid I got this result.

Putting that together with setting the figure min_border to zero, either using the kwarg or using the attribute directly p.min_border(0), I was able to remove all the space and get it to look how I wanted.

FWIW, here is the final code (which I will be adapting for my actual use case).

''' Present a scatter plot with linked histograms on both axes.

Use the ``bokeh serve`` command to run the example by executing:

    bokeh serve selection_histogram.py

at your command prompt. Then navigate to the URL

    http://localhost:5006/selection_histogram

in your browser.

'''

import numpy as np

from bokeh.layouts import gridplot
from bokeh.models import BoxSelectTool, LassoSelectTool
from bokeh.plotting import curdoc, figure

# create three normal population samples with different parameters
x1 = np.random.normal(loc=5.0, size=400) * 100
y1 = np.random.normal(loc=10.0, size=400) * 10

x2 = np.random.normal(loc=5.0, size=800) * 50
y2 = np.random.normal(loc=5.0, size=800) * 10

x3 = np.random.normal(loc=55.0, size=200) * 10
y3 = np.random.normal(loc=4.0, size=200) * 10

x = np.concatenate((x1, x2, x3))
y = np.concatenate((y1, y2, y3))

TOOLS = "pan,wheel_zoom,box_select,lasso_select,reset"

# create the scatter plot
p = figure(tools=TOOLS, plot_width=600, plot_height=600, min_border=0,
           x_axis_location=None, y_axis_location=None,
           title="Linked Histograms")
p.background_fill_color = "#fafafa"
p.select(BoxSelectTool).select_every_mousemove = False
p.select(LassoSelectTool).select_every_mousemove = False

r = p.scatter(x, y, size=3, color="#3A5785", alpha=0.6)

# create the horizontal histogram
hhist, hedges = np.histogram(x, bins=20)
hzeros = np.zeros(len(hedges)-1)
hmax = max(hhist)*1.1

LINE_ARGS = dict(color="#3A5785", line_color=None)
BK_COLOR = "#fafafa"

ph = figure(toolbar_location=None, plot_width=p.plot_width, plot_height=200,
            x_range=p.x_range, y_range=(-hmax, hmax), y_axis_location='right',
            min_border=0)
ph.background_fill_color = BK_COLOR

ph.quad(bottom=0, left=hedges[:-1], right=hedges[1:], top=hhist, color="white",
        line_color="#3A5785")
hh1 = ph.quad(bottom=0, left=hedges[:-1], right=hedges[1:], top=hzeros,
              alpha=0.5, **LINE_ARGS)
hh2 = ph.quad(bottom=0, left=hedges[:-1], right=hedges[1:], top=hzeros,
              alpha=0.1, **LINE_ARGS)

# create the vertical histogram
vhist, vedges = np.histogram(y, bins=20)
vzeros = np.zeros(len(vedges)-1)
vmax = max(vhist)*1.1

pv = figure(toolbar_location=None, plot_width=200, plot_height=p.plot_height,
            x_range=(-vmax, vmax), y_range=p.y_range, x_axis_location='above',
            min_border=0)
pv.background_fill_color = BK_COLOR

pv.quad(left=0, bottom=vedges[:-1], top=vedges[1:], right=vhist, color="white",
        line_color="#3A5785")
vh1 = pv.quad(left=0, bottom=vedges[:-1], top=vedges[1:], right=vzeros,
              alpha=0.5, **LINE_ARGS)
vh2 = pv.quad(left=0, bottom=vedges[:-1], top=vedges[1:], right=vzeros,
              alpha=0.1, **LINE_ARGS)

layout = gridplot([[pv, p], [None, ph]], merge_tools=False)

curdoc().add_root(layout)
curdoc().title = "Selection Histogram"


def update(attr, old, new):
    inds = new
    if len(inds) == 0 or len(inds) == len(x):
        hhist1, hhist2 = hzeros, hzeros
        vhist1, vhist2 = vzeros, vzeros
    else:
        neg_inds = np.ones_like(x, dtype=np.bool)
        neg_inds[inds] = False
        hhist1, _ = np.histogram(x[inds], bins=hedges)
        vhist1, _ = np.histogram(y[inds], bins=vedges)
        hhist2, _ = np.histogram(x[neg_inds], bins=hedges)
        vhist2, _ = np.histogram(y[neg_inds], bins=vedges)

    hh1.data_source.data["top"] = hhist1
    hh2.data_source.data["top"] = -hhist2
    vh1.data_source.data["right"] = vhist1
    vh2.data_source.data["right"] = -vhist2


r.data_source.selected.on_change('indices', update)
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