Plotting data with categorical x and y axes in python

Question

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.

you might want to change d to df in line 3 and 4 ? Otherwise I think this is an interesting question. I do not know why people downvoted it. — Moritz
– Moritz, Commented Jun 28, 2018 at 20:47
@Moritz. Thanks for comment. I am also wondering what is wrong with this question!!! — Masih
– Masih, Commented Jun 28, 2018 at 20:49
I wish people could explain what is wrong before downvoting!!! — Masih
– Masih, Commented Jun 28, 2018 at 20:56
@user3015703 It's likely gained down votes because it doesn't show what you've tried in order to come up with a solution on your own. — Shakes
– Shakes, Commented Jun 28, 2018 at 20:56
you might want to have a look at seaborn: seaborn.pydata.org/index.html It provides some neat features for plotting on data aware grids — Moritz
– Moritz, Commented Jun 28, 2018 at 21:03

pask · Accepted Answer · 2018-06-29 20:25:34Z

5

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.

edited Jun 29, 2018 at 20:25

answered Jun 28, 2018 at 21:20

pask

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Comments

marc_s · Accepted Answer · 2018-06-29 04:28:25Z

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()

Moritz · Accepted Answer · 2018-06-28 20:57:54Z

2

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)

answered Jun 28, 2018 at 20:57

Moritz

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2 Comments

Masih Over a year ago

I need values for each sample to be in one raw in the plot and presence/absence to be coded by different shapes. Isn't is possible to both x and y axis include categorical data?

Moritz Over a year ago

you could try a heatmap

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