Main branches regulator detection
[1]:
import matplotlib.pyplot as plt
import scanpy as sc
[2]:
import phlower
phlower.__version__
[2]:
'0.1.3'
[3]:
!mkdir save
!wget --no-check-certificate --no-verbose https://costalab.ukaachen.de/open_data/PHLOWER/multiome_phlower.pickle -O save/multiome_phlower.pickle
!wget --no-check-certificate --no-verbose https://costalab.ukaachen.de/open_data/PHLOWER/multiome_chromvar.h5 -O save/multiome_chromvar.h5
mkdir: cannot create directory ‘save’: File exists
WARNING: The certificate of ‘costalab.ukaachen.de’ is not trusted.
WARNING: The certificate of ‘costalab.ukaachen.de’ hasn't got a known issuer.
2024-10-16 15:57:35 URL:https://costalab.ukaachen.de/open_data/PHLOWER/multiome_phlower.pickle [4365968492/4365968492] -> "save/multiome_phlower.pickle" [1]
WARNING: The certificate of ‘costalab.ukaachen.de’ is not trusted.
WARNING: The certificate of ‘costalab.ukaachen.de’ hasn't got a known issuer.
2024-10-16 15:57:36 URL:https://costalab.ukaachen.de/open_data/PHLOWER/multiome_chromvar.h5 [73101100/73101100] -> "save/multiome_chromvar.h5" [1]
[4]:
import pickle as pkl
adata = pkl.load(open("save/multiome_phlower.pickle", 'rb'))
tfbdata = sc.read_10x_h5("save/multiome_chromvar.h5")
tfbdata.var_names = [i.upper() for i in tfbdata.var_names]
assert(all(tfbdata.obs_names == adata.obs_names))
import copy
tfbdata.obs = copy.deepcopy(adata.obs)
tfbdata.obsm = copy.deepcopy(adata.obsm)
tfbdata.uns = copy.deepcopy(adata.uns)
[5]:
branch_order_preference={"original": ["Podocytes", "Muscle", "Neuron-1", "Stromal-1", "Stromal-2", "Stromal-3"]}
phlower.ext.plot_stream_sc(adata, color=['group_str'], show_legend=False, s=20, dist_scale=.4, preference=branch_order_preference)
List main branches
[6]:
main_stromal = ("Stromal-1", "Stromal-2", "Stromal-3", "Stromal-4")
main_pt_podo = ("Podocytes", "Tubular")
main_neuronMuscle = ("Muscle", "Neuron-1", "Neuron-2")
Stromal main branch regulators
[7]:
phlower.tl.mbranch_regulator_detect(adata, tfbdata, branch=main_stromal, log2fc=0.3, correlation=0.7, name="stromal")
against branches [('Muscle', 'Neuron-2', 'Neuron-1'), ('Podocytes', 'Tubular')]
WARNING: Default of the method has been changed to 't-test' from 't-test_overestim_var'
vs_name: markers_stromalvs
/home/sz753404/miniconda3/envs/R422/lib/python3.10/site-packages/phlower/tools/tree_feature_markers.py:1134: ConstantInputWarning: An input array is constant; the correlation coefficient is not defined.
corr = pearsonr(expression, TF)[0]
TF markers volcano
[8]:
df = phlower.tl.get_markers_df(tfbdata, 'markers_stromalvs')
fig, ax = plt.subplots(1,1, figsize=(6, 4))
phlower.pl.volcano(df, log2fc_column='logfoldchanges', pval_column='pvals_adj',log2fc_threshold=[-.3, .3], pval_threshold=0.05, is_adjust_text=True, text_size=10, text_up_down='up', ax=ax, show_legend=False)
TF gene correlations
[9]:
_, ax = plt.subplots(1,1,figsize=(5,6))
phlower.pl.regulator_dot_correlation(tfbdata, 'stromal', ax=ax)
Heatmap along main trajectory
[10]:
_,axes = phlower.pl.regulator_heatmap(adata, tfbdata, 'stromal', figsize=(10, 7))
Podocytes & Tubular main branch regulators
[11]:
phlower.tl.mbranch_regulator_detect(adata, tfbdata, branch=main_pt_podo, log2fc=0.5, correlation=0.7, name="epi")
against branches [('Stromal-2', 'Stromal-4', 'Stromal-1', 'Stromal-3'), ('Muscle', 'Neuron-2', 'Neuron-1')]
WARNING: Default of the method has been changed to 't-test' from 't-test_overestim_var'
vs_name: markers_epivs
/home/sz753404/miniconda3/envs/R422/lib/python3.10/site-packages/phlower/tools/tree_feature_markers.py:1134: ConstantInputWarning: An input array is constant; the correlation coefficient is not defined.
corr = pearsonr(expression, TF)[0]
[12]:
df = phlower.tl.get_markers_df(tfbdata, 'markers_epivs')
fig, ax = plt.subplots(1,1, figsize=(6, 4))
phlower.pl.volcano(df, log2fc_column='logfoldchanges', pval_column='pvals_adj',log2fc_threshold=[-.3, .3], pval_threshold=0.05, is_adjust_text=True, text_size=10, text_up_down='up', ax=ax, show_legend=False)
[13]:
_, ax = plt.subplots(1,1,figsize=(5,6))
phlower.pl.regulator_dot_correlation(tfbdata, 'epi', ax=ax)
[14]:
_,axes = phlower.pl.regulator_heatmap(adata, tfbdata, 'epi', figsize=(10, 7))
Neuron & Muscle main branch regulators
[15]:
phlower.tl.mbranch_regulator_detect(adata, tfbdata, branch=main_neuronMuscle, log2fc=0.2, correlation=0.7, name="neuMsl")
against branches [('Stromal-2', 'Stromal-4', 'Stromal-1', 'Stromal-3'), ('Podocytes', 'Tubular')]
WARNING: Default of the method has been changed to 't-test' from 't-test_overestim_var'
vs_name: markers_neuMslvs
/home/sz753404/miniconda3/envs/R422/lib/python3.10/site-packages/phlower/tools/tree_feature_markers.py:1134: ConstantInputWarning: An input array is constant; the correlation coefficient is not defined.
corr = pearsonr(expression, TF)[0]
[16]:
df = phlower.tl.get_markers_df(tfbdata, 'markers_neuMslvs')
fig, ax = plt.subplots(1,1, figsize=(6, 4))
phlower.pl.volcano(df, log2fc_column='logfoldchanges', pval_column='pvals_adj',log2fc_threshold=[-.2, .2], pval_threshold=0.05, is_adjust_text=True, text_size=10, text_up_down='up', ax=ax, show_legend=False)
[17]:
_, ax = plt.subplots(1,1,figsize=(5,6))
phlower.pl.regulator_dot_correlation(tfbdata, 'neuMsl', ax=ax)
[18]:
_,axes = phlower.pl.regulator_heatmap(adata, tfbdata, 'neuMsl', figsize=(10, 7))
[19]:
import session_info
session_info.show()
[19]:
Click to view session information
----- anndata 0.9.2 matplotlib 3.9.1.post1 pandas 2.2.3 phlower 0.1.3 scanpy 1.9.3 session_info 1.0.0 -----
Click to view modules imported as dependencies
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----- IPython 8.15.0 jupyter_client 8.2.0 jupyter_core 5.3.0 jupyterlab 3.6.1 notebook 6.5.3 ----- Python 3.10.8 | packaged by conda-forge | (main, Nov 22 2022, 08:23:14) [GCC 10.4.0] Linux-4.18.0-553.5.1.el8_10.x86_64-x86_64-with-glibc2.28 ----- Session information updated at 2024-10-16 15:58