Viz LDA model with Bokeh and T-sne - python-2.7

Question

I have tried to follow this tutorial (https://shuaiw.github.io/2016/12/22/topic-modeling-and-tsne-visualzation.html) of visualizing LDA with t-sne and bokeh.
But i run into a bit of problem.
When i tried to run the following code:
plot_lda.scatter(x=tsne_lda[:, 0], y=tsne_lda[:, 1],
color=colormap[_lda_keys][:num_example],
source=bp.ColumnDataSource({
"content": text[:num_example],
"topic_key": _lda_keys[:num_example]
}))
NB: In the tutorial the content is called news, in mine it is called text
i get this error:
Supplying a user-defined data source AND iterable values to glyph methods is
not possibe. Either:
Pass all data directly as literals:
p.circe(x=a_list, y=an_array, ...)
Or, put all data in a ColumnDataSource and pass column names:
source = ColumnDataSource(data=dict(x=a_list, y=an_array))
p.circe(x='x', y='x', source=source, ...)
To me this do not make so much sense and i have not succeded in finding any annswer to it ethier here, github or else where. Hope that some on can help. best Niels

Answer 1

I've been also battling with that piece of code and I've found two problems with it.
First, when you pass a source to the scatter function, like the error states, you must include all data in the dictionary, i.e., x and y axes, colors, labels, and any other information that you want to include in the tooltip.
Second, the x and y axes have a different shape than the information passed to the tooltip, so you also have to slice both arrays in the axes with the num_example variable.
The following code got me running:
# create the dictionary with all the information
plot_dict = {
'x': tsne_lda[:num_example, 0],
'y': tsne_lda[:num_example, 1],
'colors': colormap[_lda_keys][:num_example],
'content': text[:num_example],
'topic_key': _lda_keys[:num_example]
}
# create the dataframe from the dictionary
plot_df = pd.DataFrame.from_dict(plot_dict)
# declare the source
source = bp.ColumnDataSource(data=plot_df)
title = 'LDA viz'
# initialize bokeh plot
plot_lda = bp.figure(plot_width=1400, plot_height=1100,
title=title,
tools="pan,wheel_zoom,box_zoom,reset,hover,previewsave",
x_axis_type=None, y_axis_type=None, min_border=1)
# build scatter function from the columns of the dataframe
plot_lda.scatter('x', 'y', color='colors', source=source)