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oicr-gsi / modelTsne

A t-SNE framework to visualize OMICs data
MIT License
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plotTsne() is not working #1

Open biobug16 opened 4 years ago

biobug16 commented 4 years ago

Hi @albertojleon thank you for developing and sharing such a nice package. But I am unable to use plotTsne() as it is not generating any plot as well as it is not throwing any error. Kindly look into the matter.

Thanks

biobug16 commented 4 years ago

Hi @albertojleon Do you have any updates on this?

albertojleon commented 4 years ago

Hi @biobug16 , can you provide more detailed information?

The following guidelines contain good advise on how communicate software-related issues efficiently: https://stackoverflow.com/help/how-to-ask

biobug16 commented 4 years ago

Sure @albertojleon , I am using TCGA methylation data for all the three kidney cancer and trying to plot Tsne for them. Towards this I found your code **ModleTsne pretty helpful. I followed your example code and managed to get tsne1 and tsne2 coordinates for the cancer but could not visualize the Tsne. I followed the following code:

library(TCGAbiolinks)
library(ggplot2)
library(SummarizedExperiment)
library(modelTsne)
set.seed(7)

kirc=assay(readRDS("TCGA-KIRC.RDS"))
kirp=assay(readRDS("TCGA-KIRP.RDS"))
kich=assay(readRDS("TCGA-KICH.RDS"))

data=cbind(kirc, kirp, kich)
mydata <- na.omit(data)

group<-c(rep("KIRC",485),rep("KIRP",321),rep("KICH",66))
meth<-selectVariables(data=mydata, method="IQR", no.variables=20000)
tsne<-modelTsne(data=meth, perplexity=30, group=group)

but the code given below did not generate the plot. plotTsne(model=tsne, method="plotly", title="modelTsne example #1") It also did not throw any error. Can you please help?

biobug16 commented 4 years ago

Hi @albertojleon Looking for your kind reply.

Thanks