Investigating Gene Pathway Enrichment with Spectra
This notebook uses Spectra to translate raw gene expression into interpretable biological scores. It then uses those scores to test the hypothesis that specific ESR1 perturbations alter cell cycle transitions. The results suggest a detailed look at how different promoters or guides for the same target gene might result in different phenotypic (biological program) outcomes.
[1]:
#read in the
#import packages
import numpy as np
import json
import scanpy as sc
from collections import OrderedDict
import scipy
import pandas as pd
import matplotlib.pyplot as plt
#spectra imports
import Spectra as spc
from Spectra import Spectra_util as spc_tl
from Spectra import K_est as kst
from Spectra import default_gene_sets
import anndata as ad
[2]:
#form a location
loc="alt-prom-crispr-fiveprime/"
#load adata
adata = ad.read_h5ad(loc+"files/adata_normalised_cellcycle.h5ad")
adata.X=adata.layers["log1p"]
[3]:
annotations = spc.default_gene_sets.load()
#fit the model (We will run this with only 2 epochs to decrease runtime in this tutorial)
model_global = spc.est_spectra(adata = adata, gene_set_dictionary = annotations['global'], # because we do not use the cell types
# we will supply a regular dict
# instead of the nested dict above
use_highly_variable = True, cell_type_key =None, #"cell_type_annotations" ,
use_weights = True, lam = 0.1,
delta=0.001,
kappa = None , #change to None 0.00001
rho = 0.001, #rho 0.00001
use_cell_types = False, #set to False to not use the cell type annotations
n_top_vals = 25, #number set to 50
clean_gs=True,
label_factors=True,
num_epochs=10000,
overlap_threshold=0.2,
min_gs_num = 3
)
Cell type labels in gene set annotation dictionary and AnnData object are identical
removing gene set all_Beta-Ala_metabolism for cell type global which is of length 7 2 genes are found in the data. minimum length is 3
removing gene set all_ascorbate-uptake for cell type global which is of length 3 2 genes are found in the data. minimum length is 3
Your gene set annotation dictionary is now correctly formatted.
100%|██████████| 10000/10000 [2:05:26<00:00, 1.33it/s]
/Users/helenking/anaconda3/envs/apu/lib/python3.12/site-packages/Spectra/Spectra.py:1340: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'BTD' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
df.iloc[i,j] = id2word[idx_matrix[i,j]]
/Users/helenking/anaconda3/envs/apu/lib/python3.12/site-packages/Spectra/Spectra.py:1340: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'HLCS' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
df.iloc[i,j] = id2word[idx_matrix[i,j]]
/Users/helenking/anaconda3/envs/apu/lib/python3.12/site-packages/Spectra/Spectra.py:1340: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'TECR' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
df.iloc[i,j] = id2word[idx_matrix[i,j]]
/Users/helenking/anaconda3/envs/apu/lib/python3.12/site-packages/Spectra/Spectra.py:1340: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'TFRC' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
df.iloc[i,j] = id2word[idx_matrix[i,j]]
/Users/helenking/anaconda3/envs/apu/lib/python3.12/site-packages/Spectra/Spectra.py:1340: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'P4HB' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
df.iloc[i,j] = id2word[idx_matrix[i,j]]
/Users/helenking/anaconda3/envs/apu/lib/python3.12/site-packages/Spectra/Spectra.py:1340: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'CDH1' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
df.iloc[i,j] = id2word[idx_matrix[i,j]]
/Users/helenking/anaconda3/envs/apu/lib/python3.12/site-packages/Spectra/Spectra.py:1340: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'HSPA5' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
df.iloc[i,j] = id2word[idx_matrix[i,j]]
/Users/helenking/anaconda3/envs/apu/lib/python3.12/site-packages/Spectra/Spectra.py:1340: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'CTSD' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
df.iloc[i,j] = id2word[idx_matrix[i,j]]
/Users/helenking/anaconda3/envs/apu/lib/python3.12/site-packages/Spectra/Spectra.py:1340: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'PDIA6' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
df.iloc[i,j] = id2word[idx_matrix[i,j]]
/Users/helenking/anaconda3/envs/apu/lib/python3.12/site-packages/Spectra/Spectra.py:1340: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'SCD' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
df.iloc[i,j] = id2word[idx_matrix[i,j]]
/Users/helenking/anaconda3/envs/apu/lib/python3.12/site-packages/Spectra/Spectra.py:1340: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'BMP7' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
df.iloc[i,j] = id2word[idx_matrix[i,j]]
/Users/helenking/anaconda3/envs/apu/lib/python3.12/site-packages/Spectra/Spectra.py:1340: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'IGFBP2' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
df.iloc[i,j] = id2word[idx_matrix[i,j]]
/Users/helenking/anaconda3/envs/apu/lib/python3.12/site-packages/Spectra/Spectra.py:1340: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'SLC5A6' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
df.iloc[i,j] = id2word[idx_matrix[i,j]]
/Users/helenking/anaconda3/envs/apu/lib/python3.12/site-packages/Spectra/Spectra.py:1340: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'ACSL3' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
df.iloc[i,j] = id2word[idx_matrix[i,j]]
/Users/helenking/anaconda3/envs/apu/lib/python3.12/site-packages/Spectra/Spectra.py:1340: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'ITGA2' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
df.iloc[i,j] = id2word[idx_matrix[i,j]]
/Users/helenking/anaconda3/envs/apu/lib/python3.12/site-packages/Spectra/Spectra.py:1340: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'LAMP2' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
df.iloc[i,j] = id2word[idx_matrix[i,j]]
/Users/helenking/anaconda3/envs/apu/lib/python3.12/site-packages/Spectra/Spectra.py:1340: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'CYP51A1' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
df.iloc[i,j] = id2word[idx_matrix[i,j]]
/Users/helenking/anaconda3/envs/apu/lib/python3.12/site-packages/Spectra/Spectra.py:1340: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NPY1R' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
df.iloc[i,j] = id2word[idx_matrix[i,j]]
/Users/helenking/anaconda3/envs/apu/lib/python3.12/site-packages/Spectra/Spectra.py:1340: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'EFEMP1' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
df.iloc[i,j] = id2word[idx_matrix[i,j]]
/Users/helenking/anaconda3/envs/apu/lib/python3.12/site-packages/Spectra/Spectra.py:1340: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'CKAP4' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
df.iloc[i,j] = id2word[idx_matrix[i,j]]
/Users/helenking/anaconda3/envs/apu/lib/python3.12/site-packages/Spectra/Spectra.py:1340: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'ITGB1' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
df.iloc[i,j] = id2word[idx_matrix[i,j]]
/Users/helenking/anaconda3/envs/apu/lib/python3.12/site-packages/Spectra/Spectra.py:1340: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'EPCAM' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
df.iloc[i,j] = id2word[idx_matrix[i,j]]
/Users/helenking/anaconda3/envs/apu/lib/python3.12/site-packages/Spectra/Spectra.py:1340: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'CD9' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
df.iloc[i,j] = id2word[idx_matrix[i,j]]
/Users/helenking/anaconda3/envs/apu/lib/python3.12/site-packages/Spectra/Spectra.py:1340: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'HEXB' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
df.iloc[i,j] = id2word[idx_matrix[i,j]]
/Users/helenking/anaconda3/envs/apu/lib/python3.12/site-packages/Spectra/Spectra.py:1340: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'PRDX4' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
df.iloc[i,j] = id2word[idx_matrix[i,j]]
[4]:
# KeyError: "Could not find 'umap' or 'X_umap' in .obsm"
sc.pp.neighbors(adata, use_rep='X')
sc.tl.umap(adata)
OMP: Info #276: omp_set_nested routine deprecated, please use omp_set_max_active_levels instead.
/Users/helenking/anaconda3/envs/apu/lib/python3.12/site-packages/tqdm/auto.py:21: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html
from .autonotebook import tqdm as notebook_tqdm
[10]:
dataframe_spectra=pd.DataFrame(adata.obsm["SPECTRA_cell_scores"], index=adata.obs_names, columns=adata.uns["SPECTRA_overlap"].index)
dataframe_spectra_columns=adata.uns["SPECTRA_overlap"].index
#subset the dataframe for the cellbarcodes of ESR1_P1 ESR1_P2 and nontargeting
gene="ESR1"
[11]:
dataframe_spectra
[11]:
| 0-X-global-X-all_biotin_metabolism | 1-X-global-X-all_purine_synthesis | 2-X-global-X-all_ethanol_metabolism | 3-X-global-X-all_amino-sugar-nucleotide-sugar_metabolism | 4-X-global-X-all_steroid_metabolism | 5-X-global-X-all_carnitine-shuttle | 6-X-global-X-all_TLR_signaling | 7-X-global-X-all_phosphoinositide_signaling | 8-X-global-X-all_microautophagy-lysosomal | 9-X-global-X-9 | ... | 139-X-global-X-139 | 140-X-global-X-all_galactose_metabolism | 141-X-global-X-all_MYC_targets | 142-X-global-X-all_GLU_metabolism | 143-X-global-X-all_fatty-acid_synthesis | 144-X-global-X-all_pentose-phosphate-pathway | 145-X-global-X-all_ros_response | 146-X-global-X-all_IL6-JAK-STAT3_signaling | 147-X-global-X-all_autophagy-chaperone-mediated | 148-X-global-X-148 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| GTGTGCGGTTAGTGGG-1 | 9.237579e-03 | 4.053838e-04 | 4.750246e-11 | 5.322683e-04 | 5.557497e-09 | 4.248724e-10 | 7.161847e-04 | 3.075701e-07 | 3.413473e-11 | 2.085672e-02 | ... | 6.090823e-03 | 1.323262e-10 | 0.000388 | 2.880409e-04 | 0.003124 | 0.029767 | 3.956140e-07 | 0.000363 | 0.057384 | 0.027820 |
| TCAGATGAGCATCATC-1 | 7.051101e-09 | 1.662875e-04 | 5.717598e-04 | 1.144720e-04 | 3.238609e-04 | 1.071320e-04 | 5.162545e-04 | 3.040417e-04 | 1.782021e-04 | 2.538253e-03 | ... | 4.685277e-03 | 1.341369e-10 | 0.000818 | 1.632836e-10 | 0.002828 | 0.041279 | 5.058674e-04 | 0.000398 | 0.052450 | 0.028108 |
| GCAATCACACGACGAA-1 | 2.167318e-03 | 3.691382e-04 | 4.885835e-11 | 3.279115e-04 | 4.265923e-04 | 1.508868e-04 | 3.599413e-04 | 2.189579e-04 | 1.859391e-04 | 2.479209e-03 | ... | 1.467027e-02 | 2.486610e-04 | 0.001294 | 1.383442e-04 | 0.002948 | 0.031350 | 3.599227e-04 | 0.000401 | 0.044456 | 0.027079 |
| CACACAAAGCTGCAAG-1 | 1.413153e-03 | 3.007432e-04 | 1.872481e-03 | 3.030962e-04 | 2.353136e-04 | 1.626892e-09 | 1.210399e-09 | 2.119303e-04 | 2.140315e-10 | 3.126384e-03 | ... | 4.533910e-03 | 4.900877e-10 | 0.002375 | 2.924478e-10 | 0.008609 | 0.031775 | 2.660242e-04 | 0.000281 | 0.052374 | 0.020489 |
| AGGCCACTCTTACCTA-1 | 1.927258e-10 | 2.121895e-04 | 1.418944e-03 | 3.032002e-08 | 7.462370e-04 | 3.291458e-10 | 8.620481e-04 | 6.641354e-04 | 1.497885e-09 | 2.075204e-02 | ... | 4.979285e-10 | 2.278506e-04 | 0.001540 | 2.485600e-04 | 0.007542 | 0.030187 | 2.048542e-04 | 0.000002 | 0.063139 | 0.023481 |
| ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
| TAGCCGGAGCGTAATA-1 | 7.170779e-11 | 7.430381e-07 | 1.470620e-03 | 7.200462e-09 | 2.873440e-04 | 1.814014e-04 | 5.772967e-04 | 4.233786e-09 | 4.460185e-11 | 5.374444e-03 | ... | 3.734831e-07 | 1.968945e-04 | 0.002929 | 2.826797e-04 | 0.004844 | 0.042471 | 2.920751e-04 | 0.000505 | 0.047386 | 0.015173 |
| CTTGGCTTCAGCTTAG-1 | 2.476367e-03 | 2.263839e-04 | 1.547956e-03 | 4.779655e-04 | 3.421056e-08 | 1.699237e-09 | 3.557669e-04 | 3.625548e-04 | 6.701469e-10 | 3.329656e-03 | ... | 4.498193e-07 | 1.046996e-04 | 0.001219 | 2.700598e-04 | 0.007622 | 0.046131 | 1.096286e-07 | 0.000291 | 0.000048 | 0.036125 |
| CATATGGAGGTGTTAA-1 | 2.570778e-03 | 2.000376e-04 | 1.210368e-03 | 2.292907e-04 | 3.842223e-04 | 2.233571e-10 | 2.944821e-04 | 3.124280e-04 | 3.961496e-11 | 7.104835e-03 | ... | 9.437590e-04 | 1.307871e-08 | 0.000536 | 5.709161e-04 | 0.013282 | 0.033105 | 7.381341e-04 | 0.000377 | 0.049024 | 0.026089 |
| TCTCTAAAGGAGCGTT-1 | 1.391553e-03 | 3.627104e-04 | 9.115024e-11 | 1.524916e-04 | 2.003262e-08 | 5.953464e-10 | 5.397420e-04 | 1.982464e-04 | 1.601765e-11 | 6.056628e-03 | ... | 1.611285e-06 | 3.034562e-10 | 0.000512 | 3.202521e-04 | 0.000006 | 0.045093 | 7.756426e-04 | 0.000383 | 0.055106 | 0.027756 |
| GGGAATGTCTTGACGA-1 | 2.001940e-10 | 2.734928e-04 | 1.260464e-03 | 5.065035e-04 | 2.395792e-04 | 1.043869e-04 | 3.210498e-04 | 5.566190e-04 | 4.005243e-11 | 4.522674e-07 | ... | 2.066875e-07 | 2.202848e-04 | 0.001907 | 2.936413e-04 | 0.008942 | 0.045249 | 9.947184e-04 | 0.000402 | 0.045627 | 0.018386 |
27929 rows × 149 columns
[6]:
adata.obs["target"]=adata.obs["guide_id"].str.split("_").str.get(0)
#get a list of genes
gene_list = adata.obs["target"][(adata.obs["guide_id"].str.endswith("AP"))&(adata.obs["guide_id"]!="non-targeting_Control")].drop_duplicates().values
[21]:
dataframe_spectra_gene.columns[dataframe_spectra_gene.columns.str.endswith("transition")]
[21]:
Index(['12-X-global-X-all_G2M-transition', '80-X-global-X-all_G1S-transition'], dtype='object')
[22]:
#subselect only the the index beginning with 10 and 79
#subset esr1 transtion
dataframe_spectra_gene=dataframe_spectra.merge(adata.obs, left_index=True, right_index=True)
dataframe_spectra_gene_sub=dataframe_spectra_gene[["guide_id","target","guide_identity",'12-X-global-X-all_G2M-transition','80-X-global-X-all_G1S-transition']]
dataframe_spectra_gene_sub_sub=dataframe_spectra_gene_sub[dataframe_spectra_gene_sub["guide_id"].isin(["ESR1_AP","ESR1_MP","non-targeting_Control"])].reset_index(drop=True)
dataframe_spectra_gene_sub_sub["guide_id"]=dataframe_spectra_gene_sub_sub["guide_id"].astype(str)
dataframe_spectra_gene_sub_melt=pd.melt(dataframe_spectra_gene_sub_sub, id_vars=["guide_id","target","guide_identity"], value_vars=['12-X-global-X-all_G2M-transition','80-X-global-X-all_G1S-transition'])
[23]:
dataframe_spectra_gene.columns[dataframe_spectra_gene.columns.str.contains("guide")]
[23]:
Index(['guide_identity', 'guide_read_count', 'guide_UMI_count',
'guide_coverage', 'guide_target', 'num_guides', 'ideal_guide',
'correct_num_guides', 'guide_no', 'guide_id', 'guide_assignment'],
dtype='object')
[25]:
import seaborn as sns
sns.boxplot(data=dataframe_spectra_gene_sub_melt, hue="guide_id", y="value", x="variable")
#check the statistically difference
[25]:
<Axes: xlabel='variable', ylabel='value'>
[27]:
import scipy
a=dataframe_spectra_gene_sub_melt["value"][(dataframe_spectra_gene_sub_melt["guide_id"]=="ESR1_MP")&(dataframe_spectra_gene_sub_melt["variable"]=="12-X-global-X-all_G2M-transition")]
b=dataframe_spectra_gene_sub_melt["value"][(dataframe_spectra_gene_sub_melt["guide_id"]=="ESR1_AP")&(dataframe_spectra_gene_sub_melt["variable"]=="12-X-global-X-all_G2M-transition")]
stat, pvalue = scipy.stats.ttest_ind(a, b)
pvalue
# sns.boxplot(data=dataframe_spectra_gene_sub, x="variable", y="value", hue="guide_id")
[27]:
0.1393351839024466
[28]:
# and calculate the variance per column
dataframe_spectra_five=dataframe_spectra.var(axis=0).sort_values(ascending=False).head(5)
#calculate the median value of p1
[59]:
#plot boxplot of the top 8 gene ontology
#remove columns that end with X-7 or X-124
dataframe_spectra_boxplot=dataframe_spectra[dataframe_spectra[dataframe_spectra.columns[~dataframe_spectra.columns.str.contains("132|148|25|22|28|39|114")]].mean(axis=0).sort_values(ascending=False).head(10).index].melt()
dataframe_spectra_boxplot.to_csv(loc+"files/spectra_boxplot.csv")
# dataframe_spectra_boxplot=dataframe_spectra[dataframe_spectra.mean(axis=0).sort_values(ascending=False).head(8).index].melt()
sns.boxplot(data=dataframe_spectra_boxplot, y="variable", x="value")
plt.xlabel("Spectra Score")
plt.ylabel("Specta Label")
#make prettier
plt.savefig(loc+"figures/spectra_boxplot.pdf", dpi=300, bbox_inches="tight")
[30]:
#cellcycle
cellcycle=["12-X-global-X-all_G2M-transition","80-X-global-X-all_G1S-transition"]
[31]:
mean_df_list=[]
corr_list=[]
for gene in gene_list:
gene_adata=adata[adata.obs["guide_id"].isin([gene+"_MP",gene+"_AP"]),:]
dataframe_spectra_gene=dataframe_spectra.merge(gene_adata.obs, left_index=True, right_index=True)
min_cells=min(dataframe_spectra_gene.groupby("guide_id").size())
dataframe_spectra_gene_guide=dataframe_spectra_gene.groupby("guide_id")[dataframe_spectra_columns].apply(lambda x: x.sample(min_cells))
dataframe_spectra_gene_guide.index
p1=dataframe_spectra_gene_guide.iloc[dataframe_spectra_gene_guide.index.get_level_values('guide_id') == gene+"_AP"].reset_index(drop=True)
p2=dataframe_spectra_gene_guide.iloc[dataframe_spectra_gene_guide.index.get_level_values('guide_id') == gene+"_MP"].reset_index(drop=True)
##create a new column with gene name and the correlation across all the columns
mean_df_p1=pd.DataFrame(p1[cellcycle].mean(axis=0))
mean_df_p1.columns=[gene+"_P1"]
mean_df_p2=pd.DataFrame(p2[cellcycle].mean(axis=0))
mean_df_p2.columns=[gene+"_P2"]
#merge together
mean_df=mean_df_p1.merge(mean_df_p2, left_index=True, right_index=True)
mean_df_list.append(mean_df)
correlation_df=pd.DataFrame(p1.corrwith(p2,method="spearman" ))
correlation_df.columns=[gene]
corr_list.append(correlation_df)
# df.groupby('ID')[['Val1','Val2']].corr().iloc[0::2,-1]
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:6: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
min_cells=min(dataframe_spectra_gene.groupby("guide_id").size())
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:7: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
dataframe_spectra_gene_guide=dataframe_spectra_gene.groupby("guide_id")[dataframe_spectra_columns].apply(lambda x: x.sample(min_cells))
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:6: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
min_cells=min(dataframe_spectra_gene.groupby("guide_id").size())
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:7: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
dataframe_spectra_gene_guide=dataframe_spectra_gene.groupby("guide_id")[dataframe_spectra_columns].apply(lambda x: x.sample(min_cells))
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:6: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
min_cells=min(dataframe_spectra_gene.groupby("guide_id").size())
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:7: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
dataframe_spectra_gene_guide=dataframe_spectra_gene.groupby("guide_id")[dataframe_spectra_columns].apply(lambda x: x.sample(min_cells))
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:6: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
min_cells=min(dataframe_spectra_gene.groupby("guide_id").size())
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:7: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
dataframe_spectra_gene_guide=dataframe_spectra_gene.groupby("guide_id")[dataframe_spectra_columns].apply(lambda x: x.sample(min_cells))
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:6: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
min_cells=min(dataframe_spectra_gene.groupby("guide_id").size())
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:7: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
dataframe_spectra_gene_guide=dataframe_spectra_gene.groupby("guide_id")[dataframe_spectra_columns].apply(lambda x: x.sample(min_cells))
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:6: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
min_cells=min(dataframe_spectra_gene.groupby("guide_id").size())
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:7: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
dataframe_spectra_gene_guide=dataframe_spectra_gene.groupby("guide_id")[dataframe_spectra_columns].apply(lambda x: x.sample(min_cells))
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:6: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
min_cells=min(dataframe_spectra_gene.groupby("guide_id").size())
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:7: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
dataframe_spectra_gene_guide=dataframe_spectra_gene.groupby("guide_id")[dataframe_spectra_columns].apply(lambda x: x.sample(min_cells))
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:6: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
min_cells=min(dataframe_spectra_gene.groupby("guide_id").size())
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:7: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
dataframe_spectra_gene_guide=dataframe_spectra_gene.groupby("guide_id")[dataframe_spectra_columns].apply(lambda x: x.sample(min_cells))
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:6: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
min_cells=min(dataframe_spectra_gene.groupby("guide_id").size())
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:7: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
dataframe_spectra_gene_guide=dataframe_spectra_gene.groupby("guide_id")[dataframe_spectra_columns].apply(lambda x: x.sample(min_cells))
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:6: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
min_cells=min(dataframe_spectra_gene.groupby("guide_id").size())
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:7: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
dataframe_spectra_gene_guide=dataframe_spectra_gene.groupby("guide_id")[dataframe_spectra_columns].apply(lambda x: x.sample(min_cells))
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:6: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
min_cells=min(dataframe_spectra_gene.groupby("guide_id").size())
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:7: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
dataframe_spectra_gene_guide=dataframe_spectra_gene.groupby("guide_id")[dataframe_spectra_columns].apply(lambda x: x.sample(min_cells))
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:6: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
min_cells=min(dataframe_spectra_gene.groupby("guide_id").size())
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:7: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
dataframe_spectra_gene_guide=dataframe_spectra_gene.groupby("guide_id")[dataframe_spectra_columns].apply(lambda x: x.sample(min_cells))
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:6: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
min_cells=min(dataframe_spectra_gene.groupby("guide_id").size())
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:7: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
dataframe_spectra_gene_guide=dataframe_spectra_gene.groupby("guide_id")[dataframe_spectra_columns].apply(lambda x: x.sample(min_cells))
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:6: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
min_cells=min(dataframe_spectra_gene.groupby("guide_id").size())
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:7: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
dataframe_spectra_gene_guide=dataframe_spectra_gene.groupby("guide_id")[dataframe_spectra_columns].apply(lambda x: x.sample(min_cells))
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:6: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
min_cells=min(dataframe_spectra_gene.groupby("guide_id").size())
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:7: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
dataframe_spectra_gene_guide=dataframe_spectra_gene.groupby("guide_id")[dataframe_spectra_columns].apply(lambda x: x.sample(min_cells))
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:6: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
min_cells=min(dataframe_spectra_gene.groupby("guide_id").size())
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:7: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
dataframe_spectra_gene_guide=dataframe_spectra_gene.groupby("guide_id")[dataframe_spectra_columns].apply(lambda x: x.sample(min_cells))
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:6: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
min_cells=min(dataframe_spectra_gene.groupby("guide_id").size())
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:7: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
dataframe_spectra_gene_guide=dataframe_spectra_gene.groupby("guide_id")[dataframe_spectra_columns].apply(lambda x: x.sample(min_cells))
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:6: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
min_cells=min(dataframe_spectra_gene.groupby("guide_id").size())
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:7: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
dataframe_spectra_gene_guide=dataframe_spectra_gene.groupby("guide_id")[dataframe_spectra_columns].apply(lambda x: x.sample(min_cells))
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:6: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
min_cells=min(dataframe_spectra_gene.groupby("guide_id").size())
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:7: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
dataframe_spectra_gene_guide=dataframe_spectra_gene.groupby("guide_id")[dataframe_spectra_columns].apply(lambda x: x.sample(min_cells))
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:6: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
min_cells=min(dataframe_spectra_gene.groupby("guide_id").size())
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:7: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
dataframe_spectra_gene_guide=dataframe_spectra_gene.groupby("guide_id")[dataframe_spectra_columns].apply(lambda x: x.sample(min_cells))
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:6: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
min_cells=min(dataframe_spectra_gene.groupby("guide_id").size())
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:7: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
dataframe_spectra_gene_guide=dataframe_spectra_gene.groupby("guide_id")[dataframe_spectra_columns].apply(lambda x: x.sample(min_cells))
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:6: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
min_cells=min(dataframe_spectra_gene.groupby("guide_id").size())
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:7: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
dataframe_spectra_gene_guide=dataframe_spectra_gene.groupby("guide_id")[dataframe_spectra_columns].apply(lambda x: x.sample(min_cells))
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:6: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
min_cells=min(dataframe_spectra_gene.groupby("guide_id").size())
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:7: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
dataframe_spectra_gene_guide=dataframe_spectra_gene.groupby("guide_id")[dataframe_spectra_columns].apply(lambda x: x.sample(min_cells))
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:6: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
min_cells=min(dataframe_spectra_gene.groupby("guide_id").size())
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:7: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
dataframe_spectra_gene_guide=dataframe_spectra_gene.groupby("guide_id")[dataframe_spectra_columns].apply(lambda x: x.sample(min_cells))
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:6: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
min_cells=min(dataframe_spectra_gene.groupby("guide_id").size())
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:7: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
dataframe_spectra_gene_guide=dataframe_spectra_gene.groupby("guide_id")[dataframe_spectra_columns].apply(lambda x: x.sample(min_cells))
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:6: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
min_cells=min(dataframe_spectra_gene.groupby("guide_id").size())
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:7: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
dataframe_spectra_gene_guide=dataframe_spectra_gene.groupby("guide_id")[dataframe_spectra_columns].apply(lambda x: x.sample(min_cells))
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:6: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
min_cells=min(dataframe_spectra_gene.groupby("guide_id").size())
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:7: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
dataframe_spectra_gene_guide=dataframe_spectra_gene.groupby("guide_id")[dataframe_spectra_columns].apply(lambda x: x.sample(min_cells))
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:6: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
min_cells=min(dataframe_spectra_gene.groupby("guide_id").size())
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:7: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
dataframe_spectra_gene_guide=dataframe_spectra_gene.groupby("guide_id")[dataframe_spectra_columns].apply(lambda x: x.sample(min_cells))
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:6: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
min_cells=min(dataframe_spectra_gene.groupby("guide_id").size())
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:7: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
dataframe_spectra_gene_guide=dataframe_spectra_gene.groupby("guide_id")[dataframe_spectra_columns].apply(lambda x: x.sample(min_cells))
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:6: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
min_cells=min(dataframe_spectra_gene.groupby("guide_id").size())
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:7: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
dataframe_spectra_gene_guide=dataframe_spectra_gene.groupby("guide_id")[dataframe_spectra_columns].apply(lambda x: x.sample(min_cells))
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:6: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
min_cells=min(dataframe_spectra_gene.groupby("guide_id").size())
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:7: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
dataframe_spectra_gene_guide=dataframe_spectra_gene.groupby("guide_id")[dataframe_spectra_columns].apply(lambda x: x.sample(min_cells))
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:6: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
min_cells=min(dataframe_spectra_gene.groupby("guide_id").size())
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:7: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
dataframe_spectra_gene_guide=dataframe_spectra_gene.groupby("guide_id")[dataframe_spectra_columns].apply(lambda x: x.sample(min_cells))
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:6: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
min_cells=min(dataframe_spectra_gene.groupby("guide_id").size())
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:7: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
dataframe_spectra_gene_guide=dataframe_spectra_gene.groupby("guide_id")[dataframe_spectra_columns].apply(lambda x: x.sample(min_cells))
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:6: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
min_cells=min(dataframe_spectra_gene.groupby("guide_id").size())
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:7: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
dataframe_spectra_gene_guide=dataframe_spectra_gene.groupby("guide_id")[dataframe_spectra_columns].apply(lambda x: x.sample(min_cells))
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:6: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
min_cells=min(dataframe_spectra_gene.groupby("guide_id").size())
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:7: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
dataframe_spectra_gene_guide=dataframe_spectra_gene.groupby("guide_id")[dataframe_spectra_columns].apply(lambda x: x.sample(min_cells))
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:6: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
min_cells=min(dataframe_spectra_gene.groupby("guide_id").size())
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:7: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
dataframe_spectra_gene_guide=dataframe_spectra_gene.groupby("guide_id")[dataframe_spectra_columns].apply(lambda x: x.sample(min_cells))
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:6: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
min_cells=min(dataframe_spectra_gene.groupby("guide_id").size())
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:7: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
dataframe_spectra_gene_guide=dataframe_spectra_gene.groupby("guide_id")[dataframe_spectra_columns].apply(lambda x: x.sample(min_cells))
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:6: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
min_cells=min(dataframe_spectra_gene.groupby("guide_id").size())
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:7: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
dataframe_spectra_gene_guide=dataframe_spectra_gene.groupby("guide_id")[dataframe_spectra_columns].apply(lambda x: x.sample(min_cells))
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:6: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
min_cells=min(dataframe_spectra_gene.groupby("guide_id").size())
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:7: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
dataframe_spectra_gene_guide=dataframe_spectra_gene.groupby("guide_id")[dataframe_spectra_columns].apply(lambda x: x.sample(min_cells))
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:6: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
min_cells=min(dataframe_spectra_gene.groupby("guide_id").size())
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:7: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
dataframe_spectra_gene_guide=dataframe_spectra_gene.groupby("guide_id")[dataframe_spectra_columns].apply(lambda x: x.sample(min_cells))
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:6: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
min_cells=min(dataframe_spectra_gene.groupby("guide_id").size())
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:7: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
dataframe_spectra_gene_guide=dataframe_spectra_gene.groupby("guide_id")[dataframe_spectra_columns].apply(lambda x: x.sample(min_cells))
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:6: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
min_cells=min(dataframe_spectra_gene.groupby("guide_id").size())
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:7: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
dataframe_spectra_gene_guide=dataframe_spectra_gene.groupby("guide_id")[dataframe_spectra_columns].apply(lambda x: x.sample(min_cells))
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:6: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
min_cells=min(dataframe_spectra_gene.groupby("guide_id").size())
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:7: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
dataframe_spectra_gene_guide=dataframe_spectra_gene.groupby("guide_id")[dataframe_spectra_columns].apply(lambda x: x.sample(min_cells))
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:6: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
min_cells=min(dataframe_spectra_gene.groupby("guide_id").size())
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:7: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
dataframe_spectra_gene_guide=dataframe_spectra_gene.groupby("guide_id")[dataframe_spectra_columns].apply(lambda x: x.sample(min_cells))
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:6: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
min_cells=min(dataframe_spectra_gene.groupby("guide_id").size())
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:7: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
dataframe_spectra_gene_guide=dataframe_spectra_gene.groupby("guide_id")[dataframe_spectra_columns].apply(lambda x: x.sample(min_cells))
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:6: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
min_cells=min(dataframe_spectra_gene.groupby("guide_id").size())
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:7: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
dataframe_spectra_gene_guide=dataframe_spectra_gene.groupby("guide_id")[dataframe_spectra_columns].apply(lambda x: x.sample(min_cells))
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:6: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
min_cells=min(dataframe_spectra_gene.groupby("guide_id").size())
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:7: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
dataframe_spectra_gene_guide=dataframe_spectra_gene.groupby("guide_id")[dataframe_spectra_columns].apply(lambda x: x.sample(min_cells))
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:6: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
min_cells=min(dataframe_spectra_gene.groupby("guide_id").size())
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:7: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
dataframe_spectra_gene_guide=dataframe_spectra_gene.groupby("guide_id")[dataframe_spectra_columns].apply(lambda x: x.sample(min_cells))
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:6: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
min_cells=min(dataframe_spectra_gene.groupby("guide_id").size())
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:7: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
dataframe_spectra_gene_guide=dataframe_spectra_gene.groupby("guide_id")[dataframe_spectra_columns].apply(lambda x: x.sample(min_cells))
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:6: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
min_cells=min(dataframe_spectra_gene.groupby("guide_id").size())
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:7: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
dataframe_spectra_gene_guide=dataframe_spectra_gene.groupby("guide_id")[dataframe_spectra_columns].apply(lambda x: x.sample(min_cells))
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:6: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
min_cells=min(dataframe_spectra_gene.groupby("guide_id").size())
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:7: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
dataframe_spectra_gene_guide=dataframe_spectra_gene.groupby("guide_id")[dataframe_spectra_columns].apply(lambda x: x.sample(min_cells))
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:6: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
min_cells=min(dataframe_spectra_gene.groupby("guide_id").size())
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:7: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
dataframe_spectra_gene_guide=dataframe_spectra_gene.groupby("guide_id")[dataframe_spectra_columns].apply(lambda x: x.sample(min_cells))
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:6: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
min_cells=min(dataframe_spectra_gene.groupby("guide_id").size())
/var/folders/r_/bqnt2f_d6919cz7v1yzx2ykc0000gn/T/ipykernel_32712/4170490404.py:7: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
dataframe_spectra_gene_guide=dataframe_spectra_gene.groupby("guide_id")[dataframe_spectra_columns].apply(lambda x: x.sample(min_cells))
[32]:
corr_df=pd.concat(corr_list, axis=1)
mean_df=pd.concat(mean_df_list, axis=1)
[33]:
#melt with index values
mean_df_melt=mean_df.reset_index().melt(id_vars="index")
mean_df_melt["gene"]=mean_df_melt["variable"].str.split("_").str.get(0)
mean_df_melt["promoter"]=mean_df_melt["variable"].str.split("_").str.get(1)
[35]:
mean_df_melt_10_pivot=pd.pivot_table(mean_df_melt[mean_df_melt["index"]=="12-X-global-X-all_G2M-transition"], values="value", index="gene", columns="promoter")
mean_df_melt_70_pivot=pd.pivot_table(mean_df_melt[mean_df_melt["index"]=="80-X-global-X-all_G1S-transition"], values="value", index="gene", columns="promoter")
[36]:
#read in the significant genes from edistance
# files/significant_genes.csv
significant_genes=pd.read_csv(loc+"files/significant_genes.csv")
[37]:
%%capture
mean_df_melt_10_pivot_sub=mean_df_melt_10_pivot[mean_df_melt_10_pivot.index.isin(significant_genes["gene"])]
mean_df_melt_10_pivot_sub.loc[:,"diff"]=(mean_df_melt_10_pivot_sub.loc[:,"P2"]-mean_df_melt_10_pivot_sub.loc[:,"P1"]).abs()
mean_df_melt_10_pivot_sub=mean_df_melt_10_pivot_sub.sort_values("diff", ascending=False)
#repeat for mean_df_melt_70_pivot
mean_df_melt_70_pivot_sub=mean_df_melt_70_pivot[mean_df_melt_70_pivot.index.isin(significant_genes["gene"])]
mean_df_melt_70_pivot_sub.loc[:,"diff"]=(mean_df_melt_70_pivot_sub.loc[:,"P2"]-mean_df_melt_70_pivot_sub.loc[:,"P1"]).abs()
mean_df_melt_70_pivot_sub=mean_df_melt_70_pivot_sub.sort_values("diff", ascending=False)
[70]:
#put the two mean_df_melt_10_pivot_sub and mean_df_melt_70_pivot_sub into file
mean_df_melt_10_pivot_sub[["P1","P2"]][mean_df_melt_10_pivot_sub.index.isin(significant_genes["gene"][significant_genes["successfulKD"]==True])].to_csv(loc+"files/mean_df_melt_10_pivot_sub.csv")
mean_df_melt_70_pivot_sub[["P1","P2"]][mean_df_melt_70_pivot_sub.index.isin(significant_genes["gene"][significant_genes["successfulKD"]==True])].to_csv(loc+"files/mean_df_melt_70_pivot_sub.csv")
[39]:
#plot two heatmaps one for index=10-X-global-X-all_G2M-transition
#two plots side by side
fig, axs = plt.subplots(ncols=2)
#make larger
fig.set_figheight(5)
#make text smaller
sns.heatmap(mean_df_melt_10_pivot_sub[["P1","P2"]][mean_df_melt_10_pivot_sub.index.isin(significant_genes["gene"])],cmap="RdBu",ax=axs[0])
#make text smaller and the size of plot smaller
sns.heatmap(mean_df_melt_70_pivot_sub[["P1","P2"]][mean_df_melt_70_pivot_sub.index.isin(significant_genes["gene"])],cmap="RdBu",ax=axs[1])
#make sma\
#title LHS B21E54 EE3968 7C53A2 33669A 3A54A5
axs[0].set_title("G2M Transition")
#title RHS
axs[1].set_title("G1S Transition")
fig.tight_layout()
plt.savefig(loc+"figures/spectra_heatmap_G2M.pdf", dpi=300, bbox_inches="tight")
[ ]:
#s
[40]:
#sort according to the mean of the P1
mean_df_melt_10_pivot=mean_df_melt_10_pivot.sort_values(by="P1", ascending=True)
mean_df_melt_70_pivot=mean_df_melt_70_pivot.sort_values(by="P1", ascending=True)
#plot two heatmaps one for index=10-X-global-X-all_G2M-transition
#two plots side by side
fig, axs = plt.subplots(ncols=2)
#make larger
fig.set_figheight(10)
#make text smaller
sns.heatmap(mean_df_melt_10_pivot,cmap="RdBu",ax=axs[0])
#make text smaller and the size of plot smaller
sns.heatmap(mean_df_melt_70_pivot, cmap="RdBu",ax=axs[1])
#make sma\
#title LHS
axs[0].set_title("G2M Transition")
#title RHS
axs[1].set_title("G1S Transition")
fig.tight_layout()
plt.savefig(loc+"figures/spectra_heatmap_G2M.pdf", dpi=300, bbox_inches="tight")
[41]:
#plot the spectra scores for the ESR1_P1, ESR1_P2 and nontargeting
fig, ax = plt.subplots(1,1, figsize=(10,40))
dataframe_spectra_esr1_melt=pd.melt(dataframe_spectra_gene, id_vars=["guide_id"], value_vars=dataframe_spectra_columns)
grouped = dataframe_spectra_esr1_melt.loc[:,['value', 'variable']].groupby(['variable']).median().sort_values(by='value')
sns.boxplot(data=dataframe_spectra_esr1_melt,y= "variable", x= "value",hue="guide_id",ax=ax,order=grouped.index)
#do
[41]:
<Axes: xlabel='value', ylabel='variable'>
[42]:
#visualize factor cell scores (this is poorly fitted bc we only ran 2 epochs)
# factor_of_interest = adata.uns['SPECTRA_overlap'].index[80]
factor_of_interest ="80-X-global-X-all_G1S-transition"
print('plotting factor:',factor_of_interest)
#add cell scores to obs
cell_scores = adata.obsm['SPECTRA_cell_scores'][:,0].astype(float)
adata.obs[factor_of_interest] = cell_scores
sc.pl.umap(adata,color=factor_of_interest,s=30,vmax=np.quantile(cell_scores,0.98))
plotting factor: 80-X-global-X-all_G1S-transition
[43]:
factors = adata.uns['SPECTRA_factors'] # factors x genes matrix that tells you how important each gene is to the resulting factors
markers = adata.uns['SPECTRA_markers'] # factors x n_top_vals list of n_top_vals top markers per factor
cell_scores = adata.obsm['SPECTRA_cell_scores'] # cells x factors matrix of cell scores
vocab = adata.var['spectra_vocab'] # boolean matrix of size # of genes that indicates the set of genes used to fit spectra
sns.heatmap(adata.uns['SPECTRA_overlap']) # overlap matrix of size factors x factors that tells you how much each factor overlaps with each other factor
[43]:
<Axes: >
[44]:
#subset esr1 only
adata_esr1 = adata[adata.obs["guide_id"].isin(["ESR1_MP","ESR1_AP","non-targeting_Control"])]
#plot
sc.pl.umap(adata_esr1,color=["guide_id","80-X-global-X-all_G1S-transition"],s=30,vmax=np.quantile(cell_scores,0.98))
/Users/helenking/anaconda3/envs/apu/lib/python3.12/site-packages/scanpy/plotting/_utils.py:487: ImplicitModificationWarning: Trying to modify attribute `._uns` of view, initializing view as actual.
adata.uns[value_to_plot + "_colors"] = colors_list
