I have a multi index dataframe, with the two indices being Sample and Lithology
Sample 20EC-P 20EC-8 20EC-10-1 ... 20EC-43 20EC-45 20EC-54
Lithology Pd Di-Grd Gb ... Hbl Plag Pd Di-Grd Gb
Rb 7.401575 39.055118 6.456693 ... 0.629921 56.535433 11.653543
Ba 24.610102 43.067678 10.716841 ... 1.073115 58.520532 56.946630
Th 3.176471 19.647059 3.647059 ... 0.823529 29.647059 5.294118
I am trying to put it into a seaborn lineplot as such.
spider = sns.lineplot(data = data, hue = data.columns.get_level_values("Lithology"),
style = data.columns.get_level_values("Sample"),
dashes = False, palette = "deep")
The lineplot comes out as
1
I have two issues. First, I want to format hues by lithology and style by sample. Outside of the lineplot function, I can successfully access sample and lithology using data.columns.get_level_values, but in the lineplot they don't seem to do anything and I haven't figured out another way to access these values. Also, the lineplot reorganizes the x-axis by alphabetical order. I want to force it to keep the same order as the dataframe, but I don't see any way to do this in the documentation.
To use hue= and style=, seaborn prefers it's dataframes in long form. pd.melt() will combine all columns and create new columns with the old column names, and a column for the values. The index too needs to be converted to a regular column (with .reset_index()).
Most seaborn functions use order= to set an order on the x-values, but with lineplot the only way is to make the column categorical applying a fixed order.
from matplotlib import pyplot as plt
import seaborn as sns
import pandas as pd
import numpy as np
column_tuples = [('20EC-P', 'Pd '), ('20EC-8', 'Di-Grd'), ('20EC-10-1 ', 'Gb'),
('20EC-43', 'Hbl Plag Pd'), ('20EC-45', 'Di-Grd'), ('20EC-54', 'Gb')]
col_index = pd.MultiIndex.from_tuples(column_tuples, names=["Sample", "Lithology"])
data = pd.DataFrame(np.random.uniform(0, 50, size=(3, len(col_index))), columns=col_index, index=['Rb', 'Ba', 'Th'])
data_long = data.melt(ignore_index=False).reset_index()
data_long['index'] = pd.Categorical(data_long['index'], data.index) # make categorical, use order of the original dataframe
ax = sns.lineplot(data=data_long, x='index', y='value',
hue="Lithology", style="Sample", dashes=False, markers=True, palette="deep")
ax.set_xlabel('')
ax.legend(loc='upper left', bbox_to_anchor=(1.01, 1.02))
plt.tight_layout() # fit legend and labels into the figure
plt.show()
The long dataframe looks like:
index Sample Lithology value
0 Rb 20EC-P Pd 6.135005
1 Ba 20EC-P Pd 6.924961
2 Th 20EC-P Pd 44.270570
...
Related
I have the very simple dataset in a csv file
condition,method,error
Normalized,LinfPGD,100
Integer,LinfPGD,100
Print+Scan(U),LinfPGD,59
Print+Scan(P),LinfPGD,9
Normalized,LinfBasicInteractive,100
Integer,LinfBasicInteractive,100
Print+Scan(U),LinfBasicInteractive,69
Print+Scan(P),LinfBasicInteractive,9
I would like to plot it in a barplot in pandas, but considering the column "method" as the main result, "condition" as the sub results considering "error" as the value to be plotted.
The closest I got from this was using crosstab
data=pd.read_csv('my_results.csv', sep=",")
pd.crosstab(data['method'], data['condition']).plot.bar(color=('DarkBlue', 'LightBlue', 'Teal'))
plt.tight_layout()
plt.show()
which returns me this
This is not what I want, because crosstab counts the number of each "condition" and I don't want that. All I want is to plot the column "error" for each "condition" considering each "method". I would also like to put the value on top of each bar. How to do that with Pandas/Matplotlib/Seaborn?
You can create a seaborn barplot directly from the original dataframe:
from matplotlib import pyplot as plt
import seaborn as sns
import pandas as pd
from io import StringIO
data_str = '''condition,method,error
Normalized,LinfPGD,100
Integer,LinfPGD,100
Print+Scan(U),LinfPGD,59
Print+Scan(P),LinfPGD,9
Normalized,LinfBasicInteractive,100
Integer,LinfBasicInteractive,100
Print+Scan(U),LinfBasicInteractive,69
Print+Scan(P),LinfBasicInteractive,9'''
data = pd.read_csv(StringIO(data_str), delimiter=',')
plt.figure(figsize=(12, 4))
sns.set_style('darkgrid')
ax = sns.barplot(data=data, x='method', y='error', hue='condition', palette=['darkblue', 'lightblue', 'teal'])
for bars in ax.containers:
ax.bar_label(bars)
ax.margins(y=0.1) # some extra space for the labels
plt.tight_layout()
plt.show()
I think we can use Pivot to transform the data frame and create a graph.
data = data.pivot(index='method', columns='condition', values='error')
data.plot.bar(color=('DarkBlue', 'LightBlue', 'Teal'))
I have a dataframe with 3 variables:
data= [["2019/oct",10,"Approved"],["2019/oct",20,"Approved"],["2019/oct",30,"Approved"],["2019/oct",40,"Approved"],["2019/nov",20,"Under evaluation"],["2019/dec",30,"Aproved"]]
df = pd.DataFrame(data, columns=['Period', 'Observations', 'Result'])
I want a barplot grouped by the Period column, showing all the values ​​contained in the Observations column and colored with the Result column.
How can I do this?
I tried the sns.barplot, but it joined the values in Observations column in just one bar(mean of the values).
sns.barplot(x='Period',y='Observations',hue='Result',data=df,ci=None)
Plot output
Assuming that you want one bar for each row, you can do as follows:
import matplotlib.pyplot as plt
import matplotlib.patches as mpatches
result_cat = df["Result"].astype("category")
result_codes = result_cat.cat.codes.values
cmap = plt.cm.Dark2(range(df["Result"].unique().shape[0]))
patches = []
for code in result_cat.cat.codes.unique():
cat = result_cat.cat.categories[code]
patches.append(mpatches.Patch(color=cmap[code], label=cat))
df.plot.bar(x='Period',
y='Observations',
color=cmap[result_codes],
legend=False)
plt.ylabel("Observations")
plt.legend(handles=patches)
If you would like it grouped by the months, and then stacked, please use the following (note I updated your code to make sure one month had more than one status), but not sure I completely understood your question correctly:
%matplotlib inline
import pandas as pd
import matplotlib.pyplot as plt
data= [["2019/oct",10,"Approved"],["2019/oct",20,"Approved"],["2019/oct",30,"Approved"],["2019/oct",40,"Under evaluation"],["2019/nov",20,"Under evaluation"],["2019/dec",30,"Aproved"]]
df = pd.DataFrame(data, columns=['Period', 'Observations', 'Result'])
df.groupby(['Period', 'Result'])['Observations'].sum().unstack('Result').plot(kind='bar', stacked=True)
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)
Problem: I have timeseries data of several days and I use sns.FacetGrid function of Seaborn python library to plot this data in facet form. In several cases, I found that mentioned seaborn function plots consecutive missing values (nan values) between two readings with a continuous line. While as matplotlib shows missing values as a gap, which makes sense. A demo example is as
import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
import seaborn as sns
# create timeseries data for 3 days such that day two contains NaN values
time_duration1 = pd.date_range('1/1/2018', periods=24,freq='H')
data1 = np.random.randn(len(time_duration1))
ds1 = pd.Series(data=data1,index=time_duration1)
time_duration2 = pd.date_range('1/2/2018',periods=24,freq='H')
data2 = [float('nan')]*len(time_duration2)
ds2 = pd.Series(data=data2,index=time_duration2)
time_duration3 = pd.date_range('1/3/2018', periods=24,freq='H')
data3 = np.random.randn(len(time_duration3))
ds3 = pd.Series(data=data3,index=time_duration3)
# combine all three days series and then convert series into pandas dataframe
DS = pd.concat([ds1,ds2,ds3])
DF = DS.to_frame()
DF.plot()
It results into following plot
Above Matplotlib plot shows missing values with a gap.
Now let us prepare same data for seaborn function as
DF['col'] = np.ones(DF.shape[0])# dummy column but required for facets
DF['timestamp'] = DF.index
DF.columns = ['data_val','col','timestamp']
g = sns.FacetGrid(DF,col='col',col_wrap=1,size=2.5)
g.map_dataframe(plt.plot,'timestamp','data_val')
See, how seaborn plot shows missing data with a line. How should I force seaborn to not plot nan values with such a line?
Note: This is a dummy example, and I need facet grid in any case to plot my data.
FacetGrid by default removes nan from the data. The reason is that some functions inside seaborn would not work properly with nans (especially some of the statistical function, I'd say).
In order to keep the nan values in the data, use the dropna=False argument to FacetGrid:
g = sns.FacetGrid(DF,... , dropna=False)
How can I achieve that using matplotlib?
Here is my code with the data you provided. As there's no class [they are all different, despite your first example in your question does have classes], I gave colors based on the numbers. You can definitely start alone from here, whatever result you want to achieve. You just need pandas, seaborn and matplotlib:
import pandas as pd
import seaborn as sns
import matplotlib.pyplot as plt
# import xls
df=pd.read_excel('data.xlsx')
# exclude Ranking values
df1 = df.ix[:,1:-1]
# for each element it takes the value of the xls cell
df2=df1.applymap(lambda x: float(x.split('\n')[1]))
# now plot it
df_heatmap = df2
fig, ax = plt.subplots(figsize=(15,15))
sns.heatmap(df_heatmap, square=True, ax=ax, annot=True, fmt="1.3f")
plt.yticks(rotation=0,fontsize=16);
plt.xticks(fontsize=12);
plt.tight_layout()
plt.savefig('dfcolorgraph.png')
Which produces the following picture.