I am making a pca bi-plot in python with Bokeh. I want to make to add text into the figure so that it more or less looks like in the image (ignoring the red lines):
).
However I can not figure out how to do this in Bokeh.
If I try to make one data source like this:
data = {'PC1': x_scale*xs, 'PC2': y_scale*ys , 'cluster': [str(x) for x in comments_df.kmeans_10],
'C1': components[0,:], 'C2': components[1,:], 'words':wordlist}
source = ColumnDataSource(data)
It starts complaining that I have different column lengths (which I am aware of). And it will not create a plot
BokehUserWarning: ColumnDataSource's columns must be of the same length. Current lengths: ('C1', 5775), ('C2', 5775), ('PC1', 16555), ('PC2', 16555), ('cluster', 16555), ('words', 5775)
My other thought was to create two datasources:
data = {'PC1': x_scale*xs, 'PC2': y_scale*ys , 'cluster': [str(x) for x in comments_df.kmeans_10]}
source = ColumnDataSource(data)
data2 = {'C1': components[0,:], 'C2': components[1,:], 'words':wordlist}
source2 = ColumnDataSource(data2)
However, In this case I get an error in plotting. My code:
plot = Plot(plot_width=600, plot_height=600, tools = [PanTool(), WheelZoomTool(), BoxZoomTool(), ResetTool()])
## PCA loadings
glyph = Circle(x="PC1", y="PC2", fill_color=cmap)
plot.add_glyph(source, glyph)
xaxis = LinearAxis()
plot.add_layout(xaxis, 'below')
plot.xaxis.axis_label = 'PC1'
yaxis = LinearAxis()
plot.add_layout(yaxis, 'left')
plot.yaxis.axis_label = 'PC2'
plot.add_layout(Grid(dimension=0, ticker=xaxis.ticker))
plot.add_layout(Grid(dimension=1, ticker=yaxis.ticker))
## PCA components
word_glyph = Text(x="C1", y="C2", text="words", text_color="red")
plot.add_glyph(source2, glyph)
# Show
show(plot)
The error:
ERROR:bokeh.core.validation.check:E-1001 (BAD_COLUMN_NAME): Glyph refers to nonexistent column name. This could either be due to a misspelling or typo, or due to an expected column being missing. : key "fill_color" value "cluster", key "x" value "PC1" (closest match: "C1"), key "y" value "PC2" (closest match: "C2") [renderer: GlyphRenderer(id='2028', ...)]
I am probably overlooking something or searching with incorrect terms, so if anyone could tell me what to do that would be great. Thanks!
