figure cannot be saved as pdf, using png instead.

[MichaelPeibo]

...

scv.pl.velocity_embedding_stream(cdata,basis='umap',legend_loc='right margin',fontsize=20,figsize=(8,8),
                                 title='RNA Velocity Stream',smooth=.5, min_mass=1,vkey='dynamical_velocity',
                                 color = "cluster",
                                save='test.pdf',
                                )

figure cannot be saved as pdf, using png instead. saving figure to file ./figures/scvelo_test.pdf.png

Versions:

Running scvelo 0.2.2 (python 3.7.3) on 2020-09-12 18:35.

[VolkerBergen]

This is a matplotlib bug, which is caught by scvelo to then save the fig as png instead of pdf. The former works, b/c it saves it as an image, while the latter sometimes cannot handle saving thousands of stream lines in vectorized form.

[MichaelPeibo]

@VolkerBergen thanks for clarification! Any solution toscv.pl.velocity_embedding_stream so that pdf image can be an option of output?

[VolkerBergen]

You could try running %matplotlib inline right at the start of your notebook (or trying different backends).

[MichaelPeibo]

Here is my first lines of code:

from IPython.core.display import display, HTML
display(HTML("<style>.container { width:90% !important; }</style>"))
%matplotlib inline

import scvelo as scv
scv.logging.print_version()
import numpy as np
import pandas as pd
import scanpy as sc
import loompy
print(loompy.__version__)
import os
import matplotlib
import matplotlib.pyplot as plt
pd.options.display.max_columns = None
from matplotlib import rcParams

scv.settings.verbosity = 3  # show errors(0), warnings(1), info(2), hints(3)
scv.settings.set_figure_params('scvelo',dpi_save=300)  # for beautified visualization
plt.rcParams['pdf.fonttype'] = 'truetype'

Unfortunately, it did not work. The magic thing is, this bug just suddenly happened. I have no idea...

[gokceneraslan]

Is there an upstream (i.e. mpl) GitHub issue for this?

[chansigit]

the same issue, not resolved.

an alternative is to save in svg format

[MichaelPeibo]

the same issue, not resolved.

an alternative is to save in svg format

Hi, I forget how I overcome this issue, but my suggestion is to update correlated packages.

[DawnEve]

In my test, when the fig is too wide, it may output png, rather than pdf. Other samples output pdf on the same machine and same code and packages.

[Roger-GOAT]

@MichaelPeibo hi, could you remember which packages should be updated? thanks!

[MichaelPeibo]

@MichaelPeibo hi, could you remember which packages should be updated? thanks!

Hi @Roger-GOAT, I don't really remember which packages I updated. Some of them are dependent on each other, so try to make all main packages up to date. Best of luck!

[YaoXueming]

please refer to issue #85, you may save it as svg and then convert it to pdf.