On Jun 24, 2016, at 7:56 PM, Augustine Koh <[email protected]> wrote:
Thanks for replying to me and sorry for taking this long to get back to you. I was interrupted from work for a while and now am back.
Indeed, I'd be more than happy to contribute a brief write up to add to the documentation once I figure out how to generate a heatmap.
Following on your link, I cloned the repo and tried executing the heatmap.py file in the example directory, but came aross this error:
ImportError Traceback (most recent call last)
/home/xxxxxxx/bokeh/examples/charts/file/heatmap.py in <module>()
3 from bokeh.charts import HeatMap, bins, output_file, show
----> 4 from bokeh.layouts import column
5 from bokeh.palettes import RdYlGn6, RdYlGn9
6 from bokeh.sampledata.autompg import autompg
ImportError: No module named layouts
Am I missing a module in the bokeh repo?
On Friday, June 3, 2016 at 10:51:36 PM UTC-5, Bryan Van de ven wrote:
The bokeh.charts API is the newest, and it only stabilized fairly recently, around the 0.10 release. The docs you link are older than that, and refer to a version of the charts API that has been deprecated and removed for some time now. Unfortunately no one has had a chance to add a HeatMap section to the user's guide yet, but there is an example you can study at:
If you have the time and interest and wanted to write up a HeatMap section in the user's guide, after you start to use it some, that would be extremely appreciated.
> On Jun 2, 2016, at 9:37 PM, Augustine Koh <[email protected]> wrote:
> Hi everyone,
> I am having trouble creating a heat map style plot of gene activity using the HeatMap class. Currently I have read in csv data into a DataFrame and have a DataFrame that goes like
> 1534 6609
> 0 -0.5 4
> 5 -0.1 3.1
> 10 1 2.6
> 15 2 1.4
> 20 2.4 0.8
> The very top row that starts with 1534, 6609... are actually the numbers for specific genes, and each column that corresponds to each gene gives a series of values corresponding to activity levels sampled at discrete time points of 0,5,10,15,20... and so forth. As the header column (containing gene labelling numbers) and index row (containing the discrete time points) are non-strings (integers), I proceeded to cast them into string data type so that it would make it possible to plot them as the x - y axes in the heat map. However, even after doing that, and passing the values into HeatMap(), I still get the error of ValueError: expected an element of List(String), got seq with invalid items  . Does anyone know what I might be doing wrong here? Why isn't it possible for me to pass my DataFrame to HeatMap() as how it was done in the example http://bokeh.pydata.org/en/0.9.3/docs/user_guide/charts.html#heatmap ?
> Thank you.
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