I want to understand how this code can be implemented in the holoviews 1.12.7 version. I was done in depreciated version

Question

I want to understand how this code can be implemented using holoviews 1.12.7 version. I am using a depreciated version. Here is the sample code that I have run

Chromosome = hv.Dimension('chromosome', unit='-', range=(AxesDF.loc['Min','Chr'],AxesDF.loc['Max','Chr']))
TraitIndex = hv.Dimension('trait index', unit='-', range=(AxesDF.loc['Min','Trait'],AxesDF.loc['Max','Trait']))
pP = hv.Dimension(r'$\mathsf{-log(p-value)}$', unit='-', range=(AxesDF.loc['Min','pP'],AxesDF.loc['Max','pP']))

SPlot_pP_Ch = holoviews.DFrame(GWASummaryStatisticsDF[['MHPos','pP-value']], dimensions={'MHPos':Chromosome,'pP-value':pP})

SPlot_Trait_Chr = holoviews.DFrame(GWASummaryStatisticsDF[['MHPos','TraitIndex','pP-value']],dimensions={'MHPos':Chromosome,'TraitIndex':TraitIndex,'pP-value':pP})

SPlot_Trait_Chr_pP = holoviews.DFrame(GWASummaryStatisticsDF[['MHPos','TraitIndex','pP-value']],dimensions={'MHPos':Chromosome,'TraitIndex':TraitIndex,'pP-value':pP})  

### Plots to Visualise: holoviews Scatter plots ##
### Example of Dataset in ***GWASummaryStatisticsDF dataframe*** ###
        MHPos   pP-value    TraitIndex
0   1.012324e+09    8.664141    1
1   1.738541e+09    7.485851    1
2   1.738436e+09    27.525929   1
3   1.738463e+09    56.837436   1
4   1.011689e+09    7.582362    1

Error Message

Can you add a text example of your data (not an image) and explain what kind of plot you would like to create? I would like to help you and that would make it a lot easier. — Sander van den Oord, Feb 06 '20 at 08:45
Hello Sander, This is the kind of scatter plot that I would like to plot. How can I share the sample data?. I am still k\new on Stackoverflow. Thanks — Emmanuel Adonyo, Feb 06 '20 at 09:00
Here's an explanation of how people create and show data: https://stackoverflow.com/questions/20109391/how-to-make-good-reproducible-pandas-examples — Sander van den Oord, Feb 06 '20 at 09:32

Sander van den Oord · Answer 1 · 2020-02-06T09:36:56.690

Okay, below is a small example of how to create a scatter plot with holoviews. If this is different from what you have or need, try to explain as clear as possible in your question what your data looks like and what you are looking for.

The .DFrame() method doesn't exist, so that's why you are getting your error message.

# import libraries
import numpy as np
import pandas as pd

import holoviews as hv
hv.extension('bokeh')

# create example data
df = pd.DataFrame({
    'chromosome': np.random.rand(10),
    'trait_index': np.random.rand(10),
})

# create scatter plot
scatter_plot = hv.Scatter(
    data=df,
    kdims=['chromosome'],
    vdims=['trait_index'],
)

scatter_plot

Thanks let me try to implement and let you know. – Emmanuel Adonyo Feb 06 '20 at 14:46 — Emmanuel Adonyo, Feb 06 '20 at 14:46

I want to understand how this code can be implemented in the holoviews 1.12.7 version. I was done in depreciated version

1 Answers1