I have a distribution that changes over time for which I would like to plot a violin plot for each time step side-by-side using seaborn. My initial attempt failed as violinplot cannot handle a np.ndarray for the y argument:
import numpy as np
import seaborn as sns
time = np.arange(0, 10)
samples = np.random.randn(10, 200)
ax = sns.violinplot(x=time, y=samples) # Exception: Data must be 1-dimensional
The seaborn documentation has an example for a vertical violinplot grouped by a categorical variable. However, it uses a DataFrame in long format.
Do I need to convert my time series into a DataFrame as well? If so, how do I achieve this?
A closer look at the documentation made me realize that omitting the x and y argument altogether leads to the data argument being interpreted in wide-form:
import numpy as np
import seaborn as sns
import matplotlib.pyplot as plt
samples = np.random.randn(20, 10)
ax = sns.violinplot(data=samples)
plt.show()
In the violin plot documentation it says that the input x and y parameters do not have to be a data frame, but they have a restriction of having the same dimension. In addition, the variable y that you created has 10 rows and 200 columns. This is detrimental when plotting the graphics and causes a dimension problem.
I tested it and this code has no problems when reading the python file.
import numpy as np
import seaborn as sns
import pandas as pd
time = np.arange(0, 200)
samples = np.random.randn(10, 200)
for sample in samples:
ax = sns.violinplot(x=time, y=sample)
You can then group the resulting graphs using this link:
https://python-graph-gallery.com/199-matplotlib-style-sheets/
If you want to convert your data into data frames it is also possible. You just need to use pandas.
example
import pandas as pd
x = [1,2,3,4]
df = pd.DataFrame(x)
Related
I have 2 tables a 10 by 110 and a 35 by 110 and both contain random numbers from a exponential distribution function provided by my professor. The assignment is to prove the central limit theorem in statistics.
What I thought to try is:
import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
"importing data"
df1 = pd.read_excel(r'C:\Users\Henry\Desktop\n10.xlsx')
df2 = pd.read_excel(r'C:\Users\Henry\Desktop\n30.xlsx')
df1avg = pd.read_excel(r'C:\Users\Henry\Desktop\n10avg.xlsx')
df2avg = pd.read_excel(r'C:\Users\Henry\Desktop\n30avg.xlsx')
"plotting n10 histogram"
plt.hist(df1, bins=34)
plt.hist(df1avg, bins=11)
"plotting n30 histogram"
plt.hist(df2, bins=63)
plt.hist(df2avg, bins=11)
Is that ok or do I need to format the tables into a singular column, and if so what is the most efficient way to do that?
I suspect that you will want to flatten your dataframe first, as illustrated below.
import numpy as np
import matplotlib.pyplot as plt
import pandas as pd
N = np.random.exponential(1, [40, 5])
df = pd.DataFrame(N) # convert to dataframe
bin_edges = np.linspace(0,6,30)
plt.figure()
plt.hist(df, bins = bin_edges, density = True)
plt.xlabel('Value')
plt.ylabel('Probability density')
The multiple (5) colours of lines per bin shows the histograms for each column of the data frame.
Fortunately, this is not hard to adjust. You can convert the data frame to a numpy array and flatten it:
plt.hist(df.to_numpy().flatten(), bins = bin_edges, density = True)
plt.ylabel('Probability density')
plt.xlabel('Value')
So I am trying to plot correlation Matrix (already calculated) in python. the table is like below:
And I would like it to look like this:
I am using the Following code in python:
import seaborn as sn
import matplotlib.pyplot as plt
import pandas as pd
data =pd.read_excel('/Desktop/wetchimp_global/corr/correlation_matrix.xlsx')
df = pd.DataFrame(data)
print (df)
corrMatrix = data.corr()
print (corrMatrix)
sn.heatmap(corrMatrix, annot=True)
plt.show()
Note that, the matrix is ready and I don't want to calculate the correlation again! but I failed to do that. Any suggestions?
You are recalculating the correlation with the following line:
corrMatrix = data.corr()
You then go on to utilize this recalculated variable in the heatmap here:
sn.heatmap(corrMatrix, annot=True)
plt.show()
To resolve this, instead of passing in the corrMatrix value which is the recalculated value, pass the pure excel data data or df (as df is just a copy of data). Thus, all the code you should need is:
import seaborn as sn
import matplotlib.pyplot as plt
import pandas as pd
data =pd.read_excel('/Desktop/wetchimp_global/corr/correlation_matrix.xlsx')
sn.heatmap(data, annot=True)
plt.show()
Note that this assumes, however, that your data IS ready for the heatmap as you suggest. As we online do not have access to your data we cannot confirm that.
I have deleted to frist column (names) and add them later so the code is as below:
import seaborn as sn
import matplotlib.pyplot as plt
import pandas as pd
data =pd.read_excel('/Users/yousefalbuhaisi/Desktop/wetchimp_global/corr/correlation_matrix.xlsx')
fig, ax = plt.subplots(dpi=150)
y_axis_labels = ['CLC','GIEMS','GLWD','LPX_BERN','LPJ_WSL','LPJ_WHyME','SDGVM','DLEM','ORCHIDEE','CLM4ME']
sn.heatmap(data,yticklabels=y_axis_labels, annot=True)
plt.show()
and the results are:
I folks,
Consider the following example
import matplotlib.pyplot as plt
import pandas as pd
import numpy as np
fig, (ax1,ax2) = plt.subplots(2,1)
dates = pd.date_range("2018-01-01","2019-01-01",freq = "1d")
x = pd.DataFrame(index = dates, data = np.linspace(0,1,len(dates)) )
x.plot(ax=ax1)
y = np.random.random([len(dates),100]) * x.values
ax2.pcolormesh(range(len(x)), np.linspace(-1,1,100), y.T)
plt.show()
At this point, I would like the both axis (ax1,ax2) to share the x-axis, i.e. displaying proper pandas dates on the second axis. sharex=True does not seem to work. How can I achieve that? I tried different possibilities which did not work out.
Edit: Since the pandas date formatting is superior to the native matplotlib formatting, please provide me with a solution where pandas date formatting is used (for instance, zooming with an interactive environment works much better with pandas date formatting). Thanks You!
One way to do it would be to do all the plotting with matplotlib, this way there are no problems with the different time formats being used:
import matplotlib.pyplot as plt
import pandas as pd
import numpy as np
fig, (ax1,ax2) = plt.subplots(2,1, sharex='col')
dates = pd.date_range("2018-01-01","2019-01-01",freq = "1d")
x = pd.DataFrame(index = dates, data = np.linspace(0,1,len(dates)) )
#x.plot(ax=ax1)
ax1.plot(x.index, x.values)
y = np.random.random([len(dates),100]) * x.values
ax2.pcolormesh(x.index, np.linspace(-1,1,100), y.T)
fig.tight_layout()
plt.show()
This gives the following plot:
What seems to work fine is to first plot the same line into the axes that should host the image, then plot the image, then remove the line again. What this does is that it tells pandas to apply its locators and formatters to that axes; they will stay after removing the line.
import matplotlib.pyplot as plt
import pandas as pd
import numpy as np
fig, (ax1,ax2) = plt.subplots(2,1, sharex=True)
dates = pd.date_range("2018-01-01","2019-01-01",freq = "1d")
x = pd.DataFrame(index = dates, data = np.linspace(0,1,len(dates)) )
x.plot(ax=ax1)
y = np.random.random([len(dates),100]) * x.values
x.plot(ax=ax2, legend=False)
ax2.pcolormesh(dates, np.linspace(-1,1,100), y.T)
ax2.lines[0].remove()
plt.show()
Note that there may be caveats of this solution when zooming or panning. Consider it more like a hack and use it as long as it works, but don't blame anyone once it doesn't.
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)
I'm trying to plot two series and have the x-axis ticks labeled every 5 years. If I index the data with a PeriodIndex for some reason I get ticks every 10 years. If I use a list of integers to index, then it works fine. Is there a way to get the right tick labels with a PeriodIndex?
import pandas as pd
import numpy as np
import matplotlib as mpl
import matplotlib.pyplot as plt
np.random.seed(0)
idx = pd.PeriodIndex(range(2000,2021),freq='A')
data = pd.DataFrame(np.random.normal(size=(len(idx),2)),index=idx)
fig,ax = plt.subplots(1,2,figsize=(10,5))
data.loc[:,0].plot(ax=ax[0])
data.iloc[9:,1].plot(ax=ax[1])
ax[1].xaxis.set_major_locator(mpl.ticker.MultipleLocator(5))
plt.show()
idx = range(2000,2021)
The workaround I know is to convert the PeriodIndex to DatetimeIndex and then to an array of datetime.datetimeobjects and use plt.plot_date() to plot and mpl.dates.YearLocator(5) to format. This seems overly complicated.