Problem using knitter with reticulate package in rstudio with matplotlib - r

Question

To elaborate on the title,
I am using rstudio making an rmarkdown file that contains both r and python code. My configuration is below:
Running under: Windows 10 x64 (build 18363)
Matrix products: default
locale:
[1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252 LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C LC_TIME=English_United Kingdom.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] Rcpp_1.0.4.6 rstudioapi_0.11 knitr_1.28 magrittr_1.5 rappdirs_0.3.1 tidyselect_1.0.0
[7] munsell_0.5.0 lattice_0.20-38 colorspace_1.4-1 R6_2.4.1 rlang_0.4.5 dplyr_0.8.5
[13] tools_3.6.3 grid_3.6.3 gtable_0.3.0 xfun_0.12 htmltools_0.4.0 yaml_2.2.1
[19] assertthat_0.2.1 digest_0.6.25 tibble_2.1.3 lifecycle_0.2.0 crayon_1.3.4 Matrix_1.2-18
[25] purrr_0.3.3 ggplot2_3.3.0 rsconnect_0.8.16 glue_1.3.2 evaluate_0.14 rmarkdown_2.1
[31] compiler_3.6.3 pillar_1.4.3 scales_1.1.0 jsonlite_1.6.1 reticulate_1.15-9000 pkgconfig_2.0.3
The python chunk I try running is:
import scipy as sp
import numpy as np
import pandas as pd
df = pd.read_csv("D:/03 PhD Edinburgh related/OneDrive/OneDrive - University of Edinburgh/00 PhD/000 PhD Data/01 Project I Chr Hansen/20200421_analysis_pp16013/20200420_pp16013_analysis.csv")
plt.scatter(df['OD'].values, df['osmolarity.mOSM'].values,
c=df['hydrophobicity'].values,cmap='magma')
plt.xlabel('OD')
plt.ylabel('osmolarity')
plt.title('osmolarity as function of OD and Hydrophobicity')
cbar = plt.colorbar()
cbar.set_label('Hydrophobicity', rotation=270)
plt.show()
I can run the python chunk fine in rStudio and display the graph as expect.
When I try using knitter to make the document it gets to the python chunk and gives the error:
"This application failed to start because it could not find or load
the Qt platform plugin "windows" in "",
reinstalling the application may fix this problem."
This is specifically related to the part using matplotlib. I can create and display the Pandas data frame.
I have tried installing the latest version of reticulate of github.
Thank you for any help in advance.

Answer 1

In my rmarkdown file, it works fine after setting the plugin path of the conda environment being used. You can add the below r code chunk before using matplotlib for python code chunk.
library(reticulate)
py_run_string("import os as os")
py_run_string("os.environ['QT_QPA_PLATFORM_PLUGIN_PATH'] = 'C:/Users/[UserID]/Anaconda3/envs/[EnvironmentName]/Library/plugins/platforms'")

Answer 2

I have managed to find the issue in another stack overflow answer this is a duplicate.
For answer please look here.
https://stackoverflow.com/a/50711837/11076186
I basically just save my python plot and then load the saved python plot in r.