y_axis_type = 'log' appears to be breaking default zoom in bokeh 0.60

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1

I’m using bokeh 0.60 on a mac. I’ve tried on pc also. I’m using google chrome as the web browser and ipython notebook.

I’ve been trying to use y_axis_type = ‘log’ and the same for the x_axis. It appears that even though my data starts well below 1. Say .05 which is quite far in log space, bokeh’s default zoom starts the y_axis at 1. It get this right when not in log mode. I suspect the zoomer is not taking the log space into account. I’ve seen the bug in other plotting libs before. You can see in the screenshot that the output of the y.min() is ~ .05 which is much smaller than 1.0. If you pan the plot up you will see a considerable amount of data below 1.

This is the python export of the ipython notebook that produced this example:

coding: utf-8

In[56]:

from bokeh import plotting

import numpy as np

plotting.output_notebook()

import matplotlib.pyplot as plt

cmap = plt.get_cmap(‘Spectral’)

import bokeh

bokeh.version

In[54]:

x = np.exp(np.arange(100))

y = np.exp(np.random.normal(size = 100))

size = np.random.normal(size = 100)

size -= size.min()

color =cmap(np.random.normal(size = 100), bytes = True)

color = [’#%X%X%X’%tuple(c[:-1]) for c in color]

plotting.scatter(x,y, x_axis_type = ‘log’, y_axis_type = ‘log’, size = size*5, color = color)

plotting.show()

y.min()

In:

2

Tom,

I will have a look (can you make an issue on GitHub with this code and screen shot?) In the meantime, you can set the range explicitly with:

  y_range=[y.min(), y.max()]

or in completeness:

  plotting.scatter(x,y, x_axis_type = 'log', y_axis_type = 'log', y_range=[y.min(), y.max()], size = size*5, color = color)

Bryan

···

On Sep 16, 2014, at 8:51 PM, Tom <[email protected]> wrote:

I'm using bokeh 0.60 on a mac. I've tried on pc also. I'm using google chrome as the web browser and ipython notebook.

I've been trying to use y_axis_type = 'log' and the same for the x_axis. It appears that even though my data starts well below 1. Say .05 which is quite far in log space, bokeh's default zoom starts the y_axis at 1. It get this right when not in log mode. I suspect the zoomer is not taking the log space into account. I've seen the bug in other plotting libs before. You can see in the screenshot that the output of the y.min() is ~ .05 which is much smaller than 1.0. If you pan the plot up you will see a considerable amount of data below 1.

This is the python export of the ipython notebook that produced this example:

# coding: utf-8

# In[56]:

from bokeh import plotting

import numpy as np

plotting.output_notebook()

import matplotlib.pyplot as plt

cmap = plt.get_cmap('Spectral')

import bokeh

bokeh.__version__

# In[54]:

x = np.exp(np.arange(100))

y = np.exp(np.random.normal(size = 100))

size = np.random.normal(size = 100)

size -= size.min()

color =cmap(np.random.normal(size = 100), bytes = True)

color = ['#%X%X%X'%tuple(c[:-1]) for c in color]

plotting.scatter(x,y, x_axis_type = 'log', y_axis_type = 'log', size = size*5, color = color)

plotting.show()

y.min()

# In:

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3

Thanks Bryan,

That works. I’ll make an issue on git.

···

On Tuesday, September 16, 2014 9:51:14 PM UTC-4, Tom wrote:

I’m using bokeh 0.60 on a mac. I’ve tried on pc also. I’m using google chrome as the web browser and ipython notebook.

I’ve been trying to use y_axis_type = ‘log’ and the same for the x_axis. It appears that even though my data starts well below 1. Say .05 which is quite far in log space, bokeh’s default zoom starts the y_axis at 1. It get this right when not in log mode. I suspect the zoomer is not taking the log space into account. I’ve seen the bug in other plotting libs before. You can see in the screenshot that the output of the y.min() is ~ .05 which is much smaller than 1.0. If you pan the plot up you will see a considerable amount of data below 1.

This is the python export of the ipython notebook that produced this example:

coding: utf-8

In[56]:

from bokeh import plotting

import numpy as np

plotting.output_notebook()

import matplotlib.pyplot as plt

cmap = plt.get_cmap(‘Spectral’)

import bokeh

bokeh.version

In[54]:

x = np.exp(np.arange(100))

y = np.exp(np.random.normal(size = 100))

size = np.random.normal(size = 100)

size -= size.min()

color =cmap(np.random.normal(size = 100), bytes = True)

color = [‘#%X%X%X’%tuple(c[:-1]) for c in color]

plotting.scatter(x,y, x_axis_type = ‘log’, y_axis_type = ‘log’, size = size*5, color = color)

plotting.show()

y.min()

In: