Develop Reference

Can I make a pie chart based on indexes in Python?

Could you please help me if you know how to make a pie chart in Python from it?
This is a reproducible example how the df looks like. However, I have way more rows over there.
import pandas as pd
data = [["70%"], ["20%"], ["10%"]]
example = pd.DataFrame(data, columns = ['percentage'])
example.index = ['Lasiogl', 'Centella', 'Osmia']
example

You can use matplotlib to plot the pie chart using dataframe and its indexes as labels of the chart:
import matplotlib.pyplot as plt
import pandas as pd
data = ['percentage':["70%"], ["20%"], ["10%"]]
example = pd.DataFrame(data, columns = ['percentage'])
my_labels = 'Lasiogl', 'Centella', 'Osmia'
plt.pie(example,labels=my_labels,autopct='%1.1f%%')
plt.show()

Plotly graph_objects add df column to hovertemplate

I am trying to generally recreate this graph and struggling with adding a column to the hovertemplate of a plotly Scatter. Here is a working example:
import pandas as pd
import chart_studio.plotly as py
import plotly.graph_objects as go
dfs = pd.read_html('https://coronavirus.jhu.edu/data/mortality', header=0)
df = dfs[0]
percent = df['Case-Fatality'] # This is my closest guess, but isn't working
fig = go.Figure(data=go.Scatter(x=df['Confirmed'],
y = df['Deaths'],
mode='markers',
hovertext=df['Country'],
hoverlabel=dict(namelength=0),
hovertemplate = '%{hovertext}<br>Confirmed: %{x}<br>Fatalities: %{y}<br>%{percent}',
))
fig.show()
I'd like to get the column Cast-Fatality to show under {percent}
I've also tried putting in the Scatter() call a line for text = [df['Case-Fatality']], and switching {percent} to {text} as shown in this example, but this doesn't pull from the dataframe as hoped.
I've tried replotting it as a px, following this example but it throws the error dictionary changed size during iteration and I think using go may be simpler than px but I'm new to plotly.
Thanks in advance for any insight for how to add a column to the hover.

As the question asks for a solution with graph_objects, here are two that work-
Method (i)
Adding %{text} where you want the variable value to be and passing another variable called text that is a list of values needed in the go.Scatter() call. Like this-
percent = df['Case-Fatality']
hovertemplate = '%{hovertext}<br>Confirmed: %{x}<br>Fatalities: %{y}<br>%{text}',text = percent
Here is the complete code-
import pandas as pd
import plotly.graph_objects as go
dfs = pd.read_html('https://coronavirus.jhu.edu/data/mortality', header=0)
df = dfs[0]
percent = df['Case-Fatality'] # This is my closest guess, but isn't working
fig = go.Figure(data=go.Scatter(x=df['Confirmed'],
y = df['Deaths'],
mode='markers',
hovertext=df['Country'],
hoverlabel=dict(namelength=0),
hovertemplate = '%{hovertext}<br>Confirmed: %{x}<br>Fatalities: %{y}<br>%{text}',
text = percent))
fig.show()
Method (ii)
This solution requires you to see the hoverlabel as when you pass x unified to hovermode. All you need to do then is pass an invisible trace with the same x-axis and the desired y-axis values. Passing mode='none' makes it invisible. Here is the complete code-
import pandas as pd
import plotly.graph_objects as go
dfs = pd.read_html('https://coronavirus.jhu.edu/data/mortality', header=0)
df = dfs[0]
percent = df['Case-Fatality'] # This is my closest guess, but isn't working
fig = go.Figure(data=go.Scatter(x=df['Confirmed'],
y = df['Deaths'],
mode='markers',
hovertext=df['Country'],
hoverlabel=dict(namelength=0)))
fig.add_scatter(x=df.Confirmed, y=percent, mode='none')
fig.update_layout(hovermode='x unified')
fig.show()

The link you shared is broken. Are you looking for something like this?
import pandas as pd
import plotly.express as px
px.scatter(df,
x="Confirmed",
y="Deaths",
hover_name="Country",
hover_data={"Case-Fatality":True})
Then if you need to use bold or change your hover_template you can follow the last step in this answer

Drawing inspiration from another SO question/answer, I find that this is working as desired and permits adding multiple cols to the hover data:
import pandas as pd
import plotly.express as px
fig = px.scatter(df,
x="Confirmed",
y="Deaths",
hover_name="Country",
hover_data=[df['Case-Fatality'], df['Deaths/100K pop.']])
fig.show()

plotly 2 or more column based subplot

I am new to plotly and wanted to visualize some data. I got this plot. see here
But I want to get this in 2 or more column based so that it can be seen better.
Can someone help me with that. Here is my source code what I have tried:
import pandas as pd
import plotly.express as px
fig = px.scatter(data2, x = "Total_System_Cost", y= "Total_CO2_Emissions",
color="Pol_Inst", symbol="Pol_Inst",
facet_row='Technologie',width=600, height=3500)
fig.show()
And the data looks like this.here

In this case you should use facet_col and facet_col_wrap as in this example
import pandas as pd
import plotly.express as px
fig = px.scatter(data2,
x="Total_System_Cost",
y="Total_CO2_Emissions",
color="Pol_Inst",
symbol="Pol_Inst",
facet_col='Technologie',
facet_col_wrap=2, #eventually change this
)
fig.show()
If you then want to use width and height do it so according to data2['Technologie'].nunique() and the value you picked for facet_col_wrap.

Holoviews scatter plot color by categorical data

I've been trying to understand how to accomplish this very simple task of plotting two datasets, each with a different color, but nothing i found online seems to do it. Here is some sample code:
import pandas as pd
import numpy as np
import holoviews as hv
from holoviews import opts
hv.extension('bokeh')
ds1x = np.random.randn(1000)
ds1y = np.random.randn(1000)
ds2x = np.random.randn(1000) * 1.5
ds2y = np.random.randn(1000) + 1
ds1 = pd.DataFrame({'dsx' : ds1x, 'dsy' : ds1y})
ds2 = pd.DataFrame({'dsx' : ds2x, 'dsy' : ds2y})
ds1['source'] = ['ds1'] * len(ds1.index)
ds2['source'] = ['ds2'] * len(ds2.index)
ds = pd.concat([ds1, ds2])
Goal is to produce two datasets in a single frame, with a categorical column keeping track of the source. Then i try plotting a scatter plot.
scatter = hv.Scatter(ds, 'dsx', 'dsy')
scatter
And that works as expected. But i cannot seem to understand how to color the two datasets differently based on the source column. I tried the following:
scatter = hv.Scatter(ds, 'dsx', 'dsy', color='source')
scatter = hv.Scatter(ds, 'dsx', 'dsy', cmap='source')
Both throw warnings and no color. I tried this:
scatter = hv.Scatter(ds, 'dsx', 'dsy')
scatter.opts(color='source')
Which throws an error. I tried converting the thing to a Holoviews dataset, same type of thing.
Why is something that is supposed to be so simple so obscure?
P.S. Yes, i know i can split the data and overlay two scatter plots and that will give different colors. But surely there has to be a way to accomplish this based on categorical data.

You can create a scatterplot in Holoviews with different colors per category as follows. They are all elegant one-liners:
1) By simply using .hvplot() on your dataframe to do this for you.
import hvplot
import hvplot.pandas
df.hvplot(kind='scatter', x='col1', y='col2', by='category_col')
# If you are using bokeh as a backend you can also just use 'color' parameter.
# I like this one more because it creates a hv.Scatter() instead of hv.NdOverlay()
# 'category_col' is here just an extra vdim, which is used for colors
df.hvplot(kind='scatter', x='col1', y='col2', color='category_col')
2) By creating an NdOverlay scatter plot as follows:
import holoviews as hv
hv.Dataset(df).to(hv.Scatter, 'col1', 'col2').overlay('category_col')
3) Or doppler's answer slightly adjusted, which sets 'category_col' as an extra vdim and is then used for the colors:
hv.Scatter(
data=df, kdims=['col1'], vdims=['col2', 'category_col'],
).opts(color='category_col', cmap=['blue', 'orange'])
Resulting plot:
You need the following sample data if you want to use my example directly:
import numpy as np
import pandas as pd
# create sample dataframe
df = pd.DataFrame({
'col1': np.random.normal(size=30),
'col2': np.random.normal(size=30),
'category_col': np.random.choice(['category_1', 'category_2'], size=30),
})
As an extra:
I find it interesting that there are basically 2 solutions to the problem.
You can create a hv.Scatter() with the category_col as an extra vdim which provides the colors or alternatively 2 separate scatterplots which are put together by hv.NdOverlay().
In the backend the hv.Scatter() solution will look like this:
:Scatter [col1] (col2,category_col)
And the hv.NdOverlay() backend looks like this:
:NdOverlay [category_col] :Scatter [col1] (col2)

This may help: http://holoviews.org/user_guide/Style_Mapping.html
Concretely, you cannot use a dim transform on a dimension that is not declared, not obscure at all :)
scatter = hv.Scatter(ds, 'dsx', ['dsy', 'source']
).opts(color=hv.dim('source').categorize({'ds1': 'blue', 'ds2': 'orange'}))
should get you there (haven't tested it myself).
Related:
Holoviews color per category
Overlay NdOverlays while keeping color / changing marker

Plotting data with categorical x and y axes in python

I have a list of case and control samples along with the information about what characteristics are present or absent in each of them. A dataframe including the information can be generated by Pandas:
import pandas as pd
df={'Patient':[True,True,False],'Control':[False,True,False]} # Presence/absence data for three genes for each sample
df=pd.DataFrame(df)
df=df.transpose()
df.columns=['GeneA','GeneB','GeneC']
I need to visualize this data as a dotplot/scatterplot in the way that both of the x and y axis to be categorical and presence/absence to be coded by different shapes. Something like following:
Patient| x x -
Control| - x -
__________________
GeneA GeneB GeneC
I am new to Matplotlib/seaborn and I can plot simple line plots and scatter plots. But searching online I could not find any instructions or plot similar to what I need here.

A quick way would be:
import pandas as pd
import matplotlib.pyplot as plt
df={'Patient':[1,1,0],'Control':[0,1,0]} # Presence/absence data for three genes for each sample
df=pd.DataFrame(df)
df=df.transpose()
df.columns=['GeneA','GeneB','GeneC']
heatmap = plt.imshow(df)
plt.xticks(range(len(df.columns.values)), df.columns.values)
plt.yticks(range(len(df.index)), df.index)
cbar = plt.colorbar(mappable=heatmap, ticks=[0, 1], orientation='vertical')
# vertically oriented colorbar
cbar.ax.set_yticklabels(['Absent', 'Present'])
Thanks to #DEEPAK SURANA for adding labels to the colorbar.

I searched the pyplot documentation and could not find a scatter or dot plot exactly like you described. Here is my take on creating a plot that illustrates what you want. The True records are blue and the False records are red.
# creating dataframe and extra column because index is not numeric
import pandas as pd
df={'Patient':[True,True,False],
'Control':[False,True,False]}
df=pd.DataFrame(df)
df=df.transpose()
df.columns=['GeneA','GeneB','GeneC']
df['level'] = [i for i in range(0, len(df))]
print(df)
# plotting the data
import matplotlib.pyplot as plt
fig, ax = plt.subplots(figsize=(10,6))
for idx, gene in enumerate(df.columns[:-1]):
df_gene = df[[gene, 'level']]
cList = ['blue' if x == True else 'red' for x in df[gene]]
for inr_idx, lv in enumerate(df['level']):
ax.scatter(x=idx, y=lv, c=cList[inr_idx], s=20)
fig.tight_layout()
plt.yticks([i for i in range(len(df.index))], list(df.index))
plt.xticks([i for i in range(len(df.columns)-1)], list(df.columns[:-1]))
plt.show()

Something like this might work
import pandas as pd
import numpy as np
from matplotlib.ticker import FixedLocator
df={'Patient':[1,1,0],'Control':[0,1,0]} # Presence/absence data for three genes for each sample
df=pd.DataFrame(df)
df=df.transpose()
df.columns=['GeneA','GeneB','GeneC']
plot = df.T.plot()
loc = FixedLocator([0,1,2])
plot.xaxis.set_major_locator(loc)
plot.xaxis.set_ticklabels(df.columns)
look at https://matplotlib.org/examples/pylab_examples/major_minor_demo1.html
and https://matplotlib.org/api/ticker_api.html
I think you have to convert the boolean values to zeros and ones to make it work. Someting like df.astype(int)