theislab/ehrapy-reproducibility

Vectorised plots

Opened this issue · 8 comments

namsaraeva commented

For the manuscript we need fully vectorized plots.

Please save plots as pdf or svg in 300dpi resolution.

We need:

eroell commented

Thx :)
Is it also enough to just use

plt.savefig("XYZ.svg", dpi=300, ...)

? :)

VladimirShitov commented

Mine is done: https://github.com/theislab/ehrapy-reproducibility/blob/main/Supplementary_Figure_1/sup_fig_1_helvetica.pdf

The figure number was changed at some point, I'll rename directory

  • ❤️1
namsaraeva commented

For Altana (me):

  • Fig1 4MB
  • Fig2 791KB
  • Fig3 5,9MB
  • Fig4 877KB
  • Fig5 will stay the same
  • Fig6 2,8MB
  • Fig7
  • Supp1 - 582KB
  • Supp2 (@VladimirShitov will send a new pdf) 782KB
  • Supp3 @Zethson
  • Supp4 586KB
  • Supp5
  • Supp6 455KB
  • Supp7 7,9MB
  • Supp8
  • Supp9
  • Supp10D
namsaraeva commented

@Zethson @Imipenem @juzb @eroell before you generate plots via matplotlib, please make sure the text is exported in editable mode. For information, please have a look here:

https://stackoverflow.com/questions/54101529/how-can-i-export-a-matplotlib-figure-as-a-vector-graphic-with-editable-text-fiel
scverse/scanpy#1720

  • 👍1
eroell commented

Got it, so in a nutshell add

import matplotlib as mpl
mpl.rcParams['pdf.fonttype'] = 42
mpl.rcParams['ps.fonttype'] = 42

to the beginning of the notebook :)

  • 👍3
VladimirShitov commented

42 is the answer to everything

  • 😄1
namsaraeva commented

New order with fig sizes:

  • Fig1 4MB
  • Fig2 5,9MB
  • Fig3 877KB
  • Fig4
  • Fig5 2,8MB
  • Fig6 2MB
  • Supp1 582KB
  • Supp2 807KB
  • Supp3 418KB
  • Supp4 311KB
  • Supp5 709KB
  • Supp6 516KB
  • Supp7 455KB
  • Supp8 7,9MB
  • Supp9 8MB
  • Supp10 471KB