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stephenslab / fastTopics

Fast algorithms for fitting topic models and non-negative matrix factorizations to count data.
https://stephenslab.github.io/fastTopics
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Update Vignette #29

Closed nikofleischer closed 1 year ago

nikofleischer commented 2 years ago

In the vignette, the function diff_count_clusters and diff_count_analysis are called to calculate differences in gene contribution to the topics. these don't exist in the package anymore.

After some confusion I deducted that de_analysis() is the correct function name now, might be good to update.

Best and thanks for the great package, Niko

EDIT: there are more changes, I will update everything I find here :)

1) parameters for volcano_plot changed. label_above_quantile replaced by do.quantile

pcarbo commented 2 years ago

Thanks. Yes indeed the vignettes need to be updated since several major changes have been making to the interface. I unfortunately won't be able to address this immediately but I will leave this Issue open as a reminder.

pcarbo commented 1 year ago

@nikofleischer I've updated the vignettes finally. I apologize for the long delay.