no plot output with screen or saved pdf files way

[yiyelinfeng]

Hi,

when I run the example for scRNA-seq: 1.1-STREAM_scRNA-seq (Bifurcation).ipynb. the program is fine, but there is no plot show in the screen or can't save as pdf files with some Futurewarnings.such as:

st.plot_qc(adata,jitter=0.3,log_scale=[0,1,4,5],hist_plot=[0,1,4,5], save_fig=True, fig_name='qc.pdf') /home/softwares/miniconda3/envs/trajectory/lib/python3.7/site-packages/seaborn/distributions.py:2551: 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 histplot (an axes-level function for histograms). warnings.warn(msg, FutureWarning) /home/softwares/miniconda3/envs/trajectory/lib/python3.7/site-packages/seaborn/distributions.py:1649: FutureWarning: The vertical parameter is deprecated and will be removed in a future version. Assign the data to the y variable instead. warnings.warn(msg, FutureWarning) /home/softwares/miniconda3/envs/trajectory/lib/python3.7/site-packages/seaborn/distributions.py:2551: 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 histplot (an axes-level function for histograms). warnings.warn(msg, FutureWarning) /home/softwares/miniconda3/envs/trajectory/lib/python3.7/site-packages/seaborn/distributions.py:1649: FutureWarning: The vertical parameter is deprecated and will be removed in a future version. Assign the data to the y variable instead. warnings.warn(msg, FutureWarning) /home/softwares/miniconda3/envs/trajectory/lib/python3.7/site-packages/seaborn/distributions.py:2551: 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 histplot (an axes-level function for histograms). warnings.warn(msg, FutureWarning) /home/softwares/miniconda3/envs/trajectory/lib/python3.7/site-packages/seaborn/distributions.py:1649: FutureWarning: The vertical parameter is deprecated and will be removed in a future version. Assign the data to the y variable instead. warnings.warn(msg, FutureWarning) /home/softwares/miniconda3/envs/trajectory/lib/python3.7/site-packages/seaborn/distributions.py:2551: 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 histplot (an axes-level function for histograms). warnings.warn(msg, FutureWarning) /home/softwares/miniconda3/envs/trajectory/lib/python3.7/site-packages/seaborn/distributions.py:1649: FutureWarning: The vertical parameter is deprecated and will be removed in a future version. Assign the data to the y variable instead. warnings.warn(msg, FutureWarning)

so, how to fix this problem?

[yiyelinfeng]

others, there is a error: st.plot_stream(adata,root='S3',color=['label','Gata1']) Traceback (most recent call last): File "", line 1, in File "/home/softwares/miniconda3/envs/trajectory/lib/python3.7/site-packages/stream/core.py", line 3151, in plot_stream sc_i=sns.scatterplot(x=0,y=1,hue=ann,data=tmp,linewidth=0) File "/home/softwares/miniconda3/envs/trajectory/lib/python3.7/site-packages/seaborn/_decorators.py", line 46, in inner_f return f(**kwargs) File "/home/softwares/miniconda3/envs/trajectory/lib/python3.7/site-packages/seaborn/relational.py", line 798, in scatterplot alpha=alpha, x_jitter=x_jitter, y_jitter=y_jitter, legend=legend, File "/home/softwares/miniconda3/envs/trajectory/lib/python3.7/site-packages/seaborn/relational.py", line 580, in init super().init(data=data, variables=variables) File "/home/softwares/miniconda3/envs/trajectory/lib/python3.7/site-packages/seaborn/_core.py", line 604, in init self.assign_variables(data, variables) File "/home/softwares/miniconda3/envs/trajectory/lib/python3.7/site-packages/seaborn/_core.py", line 668, in assign_variables data, **variables, File "/home/softwares/miniconda3/envs/trajectory/lib/python3.7/site-packages/seaborn/_core.py", line 895, in _assign_variables_longform if val is not None and len(data) != len(val): TypeError: object of type 'int' has no len()

[huidongchen]

It seems something related to the recent update of seaborn and matplotlib.

can you check their versions and downgrade seaborn to 0.10.1 and matplotlib to 3.2.2?

[yiyelinfeng]

It works, thanks. but I would like use the python commandline, there is still no plot show on screen.