After running binarization, the system automatically chooses 50PCs and 50Perplexity as the default graph and generates all expression plots in this setting. I've visualized multiple TSNEs and think that 35PCs and 35 Perplexity after binarization gives me the "best looking" plot. I have changed the scenicOptions to set this as the following:
Now, I would like to regenerate all the expression graphs in "/output/Step4_BinaryRegulonActivity_tSNE_colByActivity" to be reflective of this setting. How can I go about doing this?
Hello,
After running binarization, the system automatically chooses 50PCs and 50Perplexity as the default graph and generates all expression plots in this setting. I've visualized multiple TSNEs and think that 35PCs and 35 Perplexity after binarization gives me the "best looking" plot. I have changed the scenicOptions to set this as the following:
scenicOptions@settings$defaultTsne$aucType <- "Binary" scenicOptions@settings$defaultTsne$dims <- 35 scenicOptions@settings$defaultTsne$perpl <- 35 saveRDS(scenicOptions, file="int/scenicOptions.Rds")
Now, I would like to regenerate all the expression graphs in "/output/Step4_BinaryRegulonActivity_tSNE_colByActivity" to be reflective of this setting. How can I go about doing this?
Thank you very much! Wisoo