[1]:

import pandas as pd
import seaborn as sns
import matplotlib.pylab as plt

Step 1, read data¶

[2]:

df = pd.read_csv("cell_count.csv")

[3]:

df.head()

[3]:

	Sample: no dex	Sample: 0.1uM dex	Sample: 1uM dex	Sample:no dex+FG	Sample:0.1uM dex+FG	Sample:0.5uM dex+FG	Sample:1uM dex+FG
0	62148	7502	2	42928.0	0	830	26
1	16184	54398	8	28.0	0	6	2
2	31780	64	42	162.0	2	4	2
3	13060	22	3940	0.0	0	6	104
4	63812	16	8	0.0	0	138	4

[4]:

df = df.fillna(0)

generate density plot for each column¶

[15]:

for c in df.columns.tolist():
    # print (c.replace(":","_").replace(" ","_"))
    plt.figure()
    sns.distplot(df[c],hist=False)
    plt.xscale("log")
    out = c.replace(":","_").replace(" ","_")
    plt.savefig(f"{out}.pdf",bbox_inches='tight')

/home/yli11/.conda/envs/captureC/lib/python3.8/site-packages/seaborn/distributions.py:2619: FutureWarning: `distplot` is a deprecated function and will be removed in a future version. Please adapt your code to use either `displot` (a figure-level function with similar flexibility) or `kdeplot` (an axes-level function for kernel density plots).
  warnings.warn(msg, FutureWarning)
/home/yli11/.conda/envs/captureC/lib/python3.8/site-packages/seaborn/distributions.py:2619: FutureWarning: `distplot` is a deprecated function and will be removed in a future version. Please adapt your code to use either `displot` (a figure-level function with similar flexibility) or `kdeplot` (an axes-level function for kernel density plots).
  warnings.warn(msg, FutureWarning)
/home/yli11/.conda/envs/captureC/lib/python3.8/site-packages/seaborn/distributions.py:2619: FutureWarning: `distplot` is a deprecated function and will be removed in a future version. Please adapt your code to use either `displot` (a figure-level function with similar flexibility) or `kdeplot` (an axes-level function for kernel density plots).
  warnings.warn(msg, FutureWarning)
/home/yli11/.conda/envs/captureC/lib/python3.8/site-packages/seaborn/distributions.py:2619: FutureWarning: `distplot` is a deprecated function and will be removed in a future version. Please adapt your code to use either `displot` (a figure-level function with similar flexibility) or `kdeplot` (an axes-level function for kernel density plots).
  warnings.warn(msg, FutureWarning)
/home/yli11/.conda/envs/captureC/lib/python3.8/site-packages/seaborn/distributions.py:2619: FutureWarning: `distplot` is a deprecated function and will be removed in a future version. Please adapt your code to use either `displot` (a figure-level function with similar flexibility) or `kdeplot` (an axes-level function for kernel density plots).
  warnings.warn(msg, FutureWarning)
/home/yli11/.conda/envs/captureC/lib/python3.8/site-packages/seaborn/distributions.py:2619: FutureWarning: `distplot` is a deprecated function and will be removed in a future version. Please adapt your code to use either `displot` (a figure-level function with similar flexibility) or `kdeplot` (an axes-level function for kernel density plots).
  warnings.warn(msg, FutureWarning)
/home/yli11/.conda/envs/captureC/lib/python3.8/site-packages/seaborn/distributions.py:2619: FutureWarning: `distplot` is a deprecated function and will be removed in a future version. Please adapt your code to use either `displot` (a figure-level function with similar flexibility) or `kdeplot` (an axes-level function for kernel density plots).
  warnings.warn(msg, FutureWarning)

../_images/jupyter_notebooks_python_seaborn_distplot_6_1.png

../_images/jupyter_notebooks_python_seaborn_distplot_6_2.png

../_images/jupyter_notebooks_python_seaborn_distplot_6_3.png

../_images/jupyter_notebooks_python_seaborn_distplot_6_4.png

../_images/jupyter_notebooks_python_seaborn_distplot_6_5.png

../_images/jupyter_notebooks_python_seaborn_distplot_6_6.png

../_images/jupyter_notebooks_python_seaborn_distplot_6_7.png

merge each density¶

[17]:

for c in df.columns.tolist():
    sns.distplot(df[c],hist=False,label=c)
plt.xscale("log")
plt.legend()
plt.savefig(f"merged_density.pdf",bbox_inches='tight')

/home/yli11/.conda/envs/captureC/lib/python3.8/site-packages/seaborn/distributions.py:2619: FutureWarning: `distplot` is a deprecated function and will be removed in a future version. Please adapt your code to use either `displot` (a figure-level function with similar flexibility) or `kdeplot` (an axes-level function for kernel density plots).
  warnings.warn(msg, FutureWarning)
/home/yli11/.conda/envs/captureC/lib/python3.8/site-packages/seaborn/distributions.py:2619: FutureWarning: `distplot` is a deprecated function and will be removed in a future version. Please adapt your code to use either `displot` (a figure-level function with similar flexibility) or `kdeplot` (an axes-level function for kernel density plots).
  warnings.warn(msg, FutureWarning)
/home/yli11/.conda/envs/captureC/lib/python3.8/site-packages/seaborn/distributions.py:2619: FutureWarning: `distplot` is a deprecated function and will be removed in a future version. Please adapt your code to use either `displot` (a figure-level function with similar flexibility) or `kdeplot` (an axes-level function for kernel density plots).
  warnings.warn(msg, FutureWarning)
/home/yli11/.conda/envs/captureC/lib/python3.8/site-packages/seaborn/distributions.py:2619: FutureWarning: `distplot` is a deprecated function and will be removed in a future version. Please adapt your code to use either `displot` (a figure-level function with similar flexibility) or `kdeplot` (an axes-level function for kernel density plots).
  warnings.warn(msg, FutureWarning)
/home/yli11/.conda/envs/captureC/lib/python3.8/site-packages/seaborn/distributions.py:2619: FutureWarning: `distplot` is a deprecated function and will be removed in a future version. Please adapt your code to use either `displot` (a figure-level function with similar flexibility) or `kdeplot` (an axes-level function for kernel density plots).
  warnings.warn(msg, FutureWarning)
/home/yli11/.conda/envs/captureC/lib/python3.8/site-packages/seaborn/distributions.py:2619: FutureWarning: `distplot` is a deprecated function and will be removed in a future version. Please adapt your code to use either `displot` (a figure-level function with similar flexibility) or `kdeplot` (an axes-level function for kernel density plots).
  warnings.warn(msg, FutureWarning)
/home/yli11/.conda/envs/captureC/lib/python3.8/site-packages/seaborn/distributions.py:2619: FutureWarning: `distplot` is a deprecated function and will be removed in a future version. Please adapt your code to use either `displot` (a figure-level function with similar flexibility) or `kdeplot` (an axes-level function for kernel density plots).
  warnings.warn(msg, FutureWarning)

../_images/jupyter_notebooks_python_seaborn_distplot_8_1.png

[29]:

# log transformation
import numpy as np
for c in df.columns.tolist():
    # print (c.replace(":","_").replace(" ","_"))
    plt.figure()
    sns.distplot(df[c].apply(lambda x:np.log2(x+1)),hist=False,label=c)
    # plt.xscale("log")
    out = c.replace(":","_").replace(" ","_")
    plt.xlim(0,25)
    plt.legend()
    plt.xlabel("log2 cell count")
    plt.savefig(f"{out}_log.pdf",bbox_inches='tight')

/home/yli11/.conda/envs/captureC/lib/python3.8/site-packages/seaborn/distributions.py:2619: FutureWarning: `distplot` is a deprecated function and will be removed in a future version. Please adapt your code to use either `displot` (a figure-level function with similar flexibility) or `kdeplot` (an axes-level function for kernel density plots).
  warnings.warn(msg, FutureWarning)
/home/yli11/.conda/envs/captureC/lib/python3.8/site-packages/seaborn/distributions.py:2619: FutureWarning: `distplot` is a deprecated function and will be removed in a future version. Please adapt your code to use either `displot` (a figure-level function with similar flexibility) or `kdeplot` (an axes-level function for kernel density plots).
  warnings.warn(msg, FutureWarning)
/home/yli11/.conda/envs/captureC/lib/python3.8/site-packages/seaborn/distributions.py:2619: FutureWarning: `distplot` is a deprecated function and will be removed in a future version. Please adapt your code to use either `displot` (a figure-level function with similar flexibility) or `kdeplot` (an axes-level function for kernel density plots).
  warnings.warn(msg, FutureWarning)
/home/yli11/.conda/envs/captureC/lib/python3.8/site-packages/seaborn/distributions.py:2619: FutureWarning: `distplot` is a deprecated function and will be removed in a future version. Please adapt your code to use either `displot` (a figure-level function with similar flexibility) or `kdeplot` (an axes-level function for kernel density plots).
  warnings.warn(msg, FutureWarning)
/home/yli11/.conda/envs/captureC/lib/python3.8/site-packages/seaborn/distributions.py:2619: FutureWarning: `distplot` is a deprecated function and will be removed in a future version. Please adapt your code to use either `displot` (a figure-level function with similar flexibility) or `kdeplot` (an axes-level function for kernel density plots).
  warnings.warn(msg, FutureWarning)
/home/yli11/.conda/envs/captureC/lib/python3.8/site-packages/seaborn/distributions.py:2619: FutureWarning: `distplot` is a deprecated function and will be removed in a future version. Please adapt your code to use either `displot` (a figure-level function with similar flexibility) or `kdeplot` (an axes-level function for kernel density plots).
  warnings.warn(msg, FutureWarning)
/home/yli11/.conda/envs/captureC/lib/python3.8/site-packages/seaborn/distributions.py:2619: FutureWarning: `distplot` is a deprecated function and will be removed in a future version. Please adapt your code to use either `displot` (a figure-level function with similar flexibility) or `kdeplot` (an axes-level function for kernel density plots).
  warnings.warn(msg, FutureWarning)

../_images/jupyter_notebooks_python_seaborn_distplot_9_1.png

../_images/jupyter_notebooks_python_seaborn_distplot_9_2.png

../_images/jupyter_notebooks_python_seaborn_distplot_9_3.png

../_images/jupyter_notebooks_python_seaborn_distplot_9_4.png

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../_images/jupyter_notebooks_python_seaborn_distplot_9_6.png

../_images/jupyter_notebooks_python_seaborn_distplot_9_7.png

[24]:

# log transformation
import numpy as np
for c in df.columns.tolist():
    sns.distplot(df[c].apply(lambda x:np.log2(x+1)),hist=False,label=c)
plt.xlim(0,25)
plt.legend()
plt.xlabel("log2 cell count")
plt.savefig(f"merged_log.pdf",bbox_inches='tight')

/home/yli11/.conda/envs/captureC/lib/python3.8/site-packages/seaborn/distributions.py:2619: FutureWarning: `distplot` is a deprecated function and will be removed in a future version. Please adapt your code to use either `displot` (a figure-level function with similar flexibility) or `kdeplot` (an axes-level function for kernel density plots).
  warnings.warn(msg, FutureWarning)
/home/yli11/.conda/envs/captureC/lib/python3.8/site-packages/seaborn/distributions.py:2619: FutureWarning: `distplot` is a deprecated function and will be removed in a future version. Please adapt your code to use either `displot` (a figure-level function with similar flexibility) or `kdeplot` (an axes-level function for kernel density plots).
  warnings.warn(msg, FutureWarning)
/home/yli11/.conda/envs/captureC/lib/python3.8/site-packages/seaborn/distributions.py:2619: FutureWarning: `distplot` is a deprecated function and will be removed in a future version. Please adapt your code to use either `displot` (a figure-level function with similar flexibility) or `kdeplot` (an axes-level function for kernel density plots).
  warnings.warn(msg, FutureWarning)
/home/yli11/.conda/envs/captureC/lib/python3.8/site-packages/seaborn/distributions.py:2619: FutureWarning: `distplot` is a deprecated function and will be removed in a future version. Please adapt your code to use either `displot` (a figure-level function with similar flexibility) or `kdeplot` (an axes-level function for kernel density plots).
  warnings.warn(msg, FutureWarning)
/home/yli11/.conda/envs/captureC/lib/python3.8/site-packages/seaborn/distributions.py:2619: FutureWarning: `distplot` is a deprecated function and will be removed in a future version. Please adapt your code to use either `displot` (a figure-level function with similar flexibility) or `kdeplot` (an axes-level function for kernel density plots).
  warnings.warn(msg, FutureWarning)
/home/yli11/.conda/envs/captureC/lib/python3.8/site-packages/seaborn/distributions.py:2619: FutureWarning: `distplot` is a deprecated function and will be removed in a future version. Please adapt your code to use either `displot` (a figure-level function with similar flexibility) or `kdeplot` (an axes-level function for kernel density plots).
  warnings.warn(msg, FutureWarning)
/home/yli11/.conda/envs/captureC/lib/python3.8/site-packages/seaborn/distributions.py:2619: FutureWarning: `distplot` is a deprecated function and will be removed in a future version. Please adapt your code to use either `displot` (a figure-level function with similar flexibility) or `kdeplot` (an axes-level function for kernel density plots).
  warnings.warn(msg, FutureWarning)

../_images/jupyter_notebooks_python_seaborn_distplot_10_1.png