I'm starting to learn a bit of python (been using R) for data analysis. I'm trying to create two plots using seaborn, but it keeps saving the second on top of the first. How do I stop this behavior?
import seaborn as sns
iris = sns.load_dataset('iris')
length_plot = sns.barplot(x='sepal_length', y='species', data=iris).get_figure()
length_plot.savefig('ex1.pdf')
width_plot = sns.barplot(x='sepal_width', y='species', data=iris).get_figure()
width_plot.savefig('ex2.pdf')
You have to start a new figure in order to do that. There are multiple ways to do that, assuming you have matplotlib. Also get rid of get_figure() and you can use plt.savefig() from there.
Method 1
Use plt.clf()
import seaborn as sns
import matplotlib.pyplot as plt
iris = sns.load_dataset('iris')
length_plot = sns.barplot(x='sepal_length', y='species', data=iris)
plt.savefig('ex1.pdf')
plt.clf()
width_plot = sns.barplot(x='sepal_width', y='species', data=iris)
plt.savefig('ex2.pdf')
Method 2
Call plt.figure() before each one
plt.figure()
length_plot = sns.barplot(x='sepal_length', y='species', data=iris)
plt.savefig('ex1.pdf')
plt.figure()
width_plot = sns.barplot(x='sepal_width', y='species', data=iris)
plt.savefig('ex2.pdf')
I agree with a previous comment that importing matplotlib.pyplot is not the best software engineering practice as it exposes the underlying library. As I was creating and saving plots in a loop, then I needed to clear the figure and found out that this can now be easily done by importing seaborn only:
since version 0.11:
import seaborn as sns
import numpy as np
data = np.random.normal(size=100)
path = "/path/to/img/plot.png"
plot = sns.displot(data) # also works with histplot() etc
plot.fig.savefig(path)
plot.fig.clf() # this clears the figure
# ... continue with next figure
alternative example with a loop:
import seaborn as sns
import numpy as np
for i in range(3):
data = np.random.normal(size=100)
path = "/path/to/img/plot2_{0:01d}.png".format(i)
plot = sns.displot(data)
plot.fig.savefig(path)
plot.fig.clf() # this clears the figure
before version 0.11 (original post):
import seaborn as sns
import numpy as np
data = np.random.normal(size=100)
path = "/path/to/img/plot.png"
plot = sns.distplot(data)
plot.get_figure().savefig(path)
plot.get_figure().clf() # this clears the figure
# ... continue with next figure
Create specific figures and plot onto them:
import seaborn as sns
iris = sns.load_dataset('iris')
length_fig, length_ax = plt.subplots()
sns.barplot(x='sepal_length', y='species', data=iris, ax=length_ax)
length_fig.savefig('ex1.pdf')
width_fig, width_ax = plt.subplots()
sns.barplot(x='sepal_width', y='species', data=iris, ax=width_ax)
width_fig.savefig('ex2.pdf')
I've found that if the interaction is turned off seaborn plot the heatmap normally.
Related
I want to change the labels [2,3,4,5] from my pie chart and instead have them say [Boomer, Gen X, Gen Y, Gen Z] respectively. I can't seem to find a direct way of doing this without changing the dataframe. Is there any way to do this by working through the code I have?
import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
import seaborn as sns
%matplotlib inline
data = df.groupby("Q10_Ans")["Q4_Agree"].count()
pie, ax = plt.subplots(figsize=[10,6])
labels = data.keys()
plt.pie(x=data, autopct="%.1f%%", explode=[0.05]*4, labels=labels, pctdistance=0.5)
plt.title("Generations that agree data visualization will help with job prospects", fontsize=14);
pie.savefig("DeliveryPieChart.png")
how about change the code
labels = data.keys()
to
labels = ['Boomer','Gen X','Gen Y','Gen Z']
I don't know the data structure of your data, so I made a sample data and created a pie chart. Please modify your code to follow this.
import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
import seaborn as sns
%matplotlib inline
# data = df.groupby("Q10_Ans")["Q4_Agree"].count()
data = pd.DataFrame({'Q10_Ans':['Boomer','Gen X','Gen Y','Gen Z'],'Q4_Agree':[2,3,4,5]})
fig, ax = plt.subplots(figsize=[10,6])
labels = data['Q10_Ans']
ax.pie(x=data['Q4_Agree'], autopct="%.1f%%", explode=[0.05]*4, labels=labels, pctdistance=0.5)
ax.set_title("Generations that agree data visualization will help with job prospects", fontsize=14);
plt.savefig("DeliveryPieChart.png")
I'm plotting time series data using seaborn lineplot (https://seaborn.pydata.org/generated/seaborn.lineplot.html), and plotting the median instead of mean. Example code:
import seaborn as sns; sns.set()
import matplotlib.pyplot as plt
fmri = sns.load_dataset("fmri")
ax = sns.lineplot(x="timepoint", y="signal", estimator = np.median, data=fmri)
I want the error bands to show the interquartile range as opposed to the confidence interval. I know I can use ci = "sd" for standard deviation, but is there a simple way to add the IQR instead? I cannot figure it out.
Thank you!
I don't know if this can be done with seaborn alone, but here's one way to do it with matplotlib, keeping the seaborn style. The describe() method conveniently provides summary statistics for a DataFrame, among them the quartiles, which we can use to plot the medians with inter-quartile-ranges.
import seaborn as sns; sns.set()
import matplotlib.pyplot as plt
fmri = sns.load_dataset("fmri")
fmri_stats = fmri.groupby(['timepoint']).describe()
x = fmri_stats.index
medians = fmri_stats[('signal', '50%')]
medians.name = 'signal'
quartiles1 = fmri_stats[('signal', '25%')]
quartiles3 = fmri_stats[('signal', '75%')]
ax = sns.lineplot(x, medians)
ax.fill_between(x, quartiles1, quartiles3, alpha=0.3);
You can calculate the median within lineplot like you have done, set ci to be none and fill in using ax.fill_between()
import numpy as np
import seaborn as sns; sns.set()
import matplotlib.pyplot as plt
fmri = sns.load_dataset("fmri")
ax = sns.lineplot(x="timepoint", y="signal", estimator = np.median,
data=fmri,ci=None)
bounds = fmri.groupby('timepoint')['signal'].quantile((0.25,0.75)).unstack()
ax.fill_between(x=bounds.index,y1=bounds.iloc[:,0],y2=bounds.iloc[:,1],alpha=0.1)
This option is possible since version 0.12 of seaborn, see here for the documentation.
pip install --upgrade seaborn
The estimator specifies the point by the name of pandas method or callable, such as 'median' or 'mean'.
The errorbar is an option to plot a distribution spread by a string, (string, number) tuple, or callable. In order to mark the median value and fill the area between the interquartile, you would need the params:
import seaborn as sns; sns.set()
import matplotlib.pyplot as plt
fmri = sns.load_dataset("fmri")
ax = sns.lineplot(data=fmri, x="timepoint", y="signal", estimator=np.median,
errorbar=lambda x: (np.quantile(x, 0.25), np.quantile(x, 0.75)))
You can now!
estimator="median", errobar=("pi",0.5)
https://seaborn.pydata.org/tutorial/error_bars
I have a scatter plot im working with and for some reason im not seeing all the x values on my graph
#%%
from pandas import DataFrame, read_csv
import pandas as pd
import matplotlib.pyplot as plt
import seaborn as sns
file = r"re2.csv"
df = pd.read_csv(file)
#sns.set(rc={'figure.figsize':(11.7,8.27)})
g = sns.FacetGrid(df, col='city')
g.map(plt.scatter, 'type', 'price').add_legend()
This is an image of a small subset of my plots, you can see that Res is displaying, the middle bar should be displaying Con and the last would be Mlt. These are all defined in the type column from my data set but are not displaying.
Any clue how to fix?
Python is doing what you tell it to do. Just pick different features, presumably things that make more sense for plotting, if you want to generate a more interesting plots. See this generic example below.
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import seaborn as sns
sns.set_theme(style="darkgrid")
tips = sns.load_dataset("tips")
sns.relplot(x="total_bill", y="tip", hue="smoker", data=tips);
Personally, I like plotly plots, which are dynamic, more than I like seaborn plots.
https://plotly.com/python/line-and-scatter/
I want to replicate plots from this paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5000555/pdf/nihms774453.pdf I'm particularly interested in plot on page 16, right panel. I tried to do this in matplotlib but it seems to me that there is no way to access lines in linecollection.
I don't know how to change the color of the each line, according to the value at every index. I'd like to eventually get something like here: https://matplotlib.org/3.1.1/gallery/lines_bars_and_markers/multicolored_line.html but for every line, according to the data.
this is what I tried:
the data in numpy array: https://pastebin.com/B1wJu9Nd
import pandas as pd, numpy as np
import matplotlib.pyplot as plt
from matplotlib.collections import LineCollection
from matplotlib import colors as mcolors
%matplotlib inline
base_range = np.arange(qq.index.max()+1)
fig, ax = plt.subplots(figsize=(12,8))
ax.set_xlim(qq.index.min(), qq.index.max())
# ax.set_ylim(qq.columns[0], qq.columns[-1])
ax.set_ylim(-5, len(qq.columns) +5)
line_segments = LineCollection([np.column_stack([base_range, [y]*len(qq.index)]) for y in range(len(qq.columns))],
cmap='viridis',
linewidths=(5),
linestyles='solid',
)
line_segments.set_array(base_range)
ax.add_collection(line_segments)
axcb = fig.colorbar(line_segments)
plt.show()
my result:
what I want to achieve:
Normally I would increase matplotlib's global linewidths by editing the matplotlib.rcParams. This seems to work well directly with SciPy's dendrogram implementation but not with Seaborn's clustermap (which uses SciPy's dendrograms). Can anyone suggest a working method?
import matplotlib
matplotlib.rcParams['lines.linewidth'] = 10
import seaborn as sns; sns.set()
flights = sns.load_dataset("flights")
flights = flights.pivot("month", "year", "passengers")
g = sns.clustermap(flights)
This has now been addressed in a more robust way by the following merged pull request https://github.com/mwaskom/seaborn/pull/1935. I'm assuming it will be included in the release after v0.9.0.
You can control the LineCollection properties of the dendrogram by using the tree_kws parameter.
For example:
>>> import seaborn as sns
>>> iris = sns.load_dataset("iris")
>>> species = iris.pop("species")
>>> g = sns.clustermap(iris, tree_kws=dict(linewidths=1.5, colors=(0.2, 0.2, 0.4))
Would create a clustermap with 1.5 pt thick lines for the tree in an alternative dark purple color.
for newer versions of seaborn (tested with 0.7.1, 0.9.0), the lines are in a LineCollection, rather than by themselves. So their width can be changed as follows:
import seaborn as sns
import matplotlib.pyplot as plt
# load data and make clustermap
df = sns.load_dataset('iris')
g = sns.clustermap(df[['sepal_length', 'sepal_width']])
for a in g.ax_row_dendrogram.collections:
a.set_linewidth(10)
for a in g.ax_col_dendrogram.collections:
a.set_linewidth(10)
There may be an easier way to do it, but this seems to work:
import matplotlib
import seaborn as sns; sns.set()
flights = sns.load_dataset("flights")
flights = flights.pivot("month", "year", "passengers")
g = sns.clustermap(flights)
for l in g.ax_row_dendrogram.lines:
l.set_linewidth(10)
for l in g.ax_col_dendrogram.lines:
l.set_linewidth(10)
Edit This no longer works in Seaborn v. 0.7.1 (and probably some earlier versions as well); g.ax_col_dendrogram.lines now returns an empty list. I couldn't find a way to increase line width and I ended up temporarily modifying the Seaborn module. In file matrix.py, function class _DendrogramPlotter, the linewidth is hard-coded as 0.5; I modified it to 1.5:
line_kwargs = dict(linewidths=1.5, colors='k')
This worked but obviously isn't a very sustainable approach.