Unable to rotate pictures for my spatial transcriptomics data

[apsuresh]

Hello,

I am using human lymph node data from 10x visium spatial transcriptomics data set. Also, I am little new to coding. I was trying to understand the package STdeconvolve using your youtube tutorial. However, my picture of the dataset generated using MERINGUE looked flipped and rotated and some areas seemed to get cut off. I am attaching both images below for your reference. I tried changing parameters of parmfrow and using the following code however I was not succesful. Could you help me with understanding how to rotate and get the full image. pdf("output_plot.pdf", width = 8, height = 10) par(mfrow = c(1, 1), mar = c(2, 2, 2, 2)) Thank you so much for your help! Kindly let me know if you need more information.

Image of HE section

Rstudio plot

[bmill3r]

Hi @apsuresh,

Thanks for your interest in both MERINGUE and STdeconvolve - and so sorry for the delay in my response!

To help answer your question, I would recommend checking out this issue on STdeconvolve:

https://github.com/JEFworks-Lab/STdeconvolve/issues/39

Hope this helps, Brendan