Entering edit mode
3.5 years ago
LacquerHed
▴
30
I am trying to set up VisCello shiny app for hosting some of our single cell data, analyzed in Seurat:
https://github.com/qinzhu/VisCello
I am using the following code though running into a problem, the app launches however I dont see the umaps and when I click over to differential expression the app goes dark altogether. Below is my code:
library(VisCello)
library(Matrix)
library(Biobase)
library(irlba)
library(Seurat)
Data.Combined <- readRDS("/Users/rbronste/Desktop/Jesse files/Single Cell Analysis/Previous Analyses/6Samples2.rds")
fmeta <- data.frame(symbol = rownames(Data.Combined))
rownames(fmeta) <- fmeta$symbol
eset <- new("ExpressionSet",
assayData = assayDataNew("environment", exprs=Data.Combined@assays$RNA@counts,
norm_exprs = Data.Combined@assays$RNA@data),
phenoData = new("AnnotatedDataFrame", data = Data.Combined@meta.data),
featureData = new("AnnotatedDataFrame", data = fmeta))
#transferring embeddings to table for VisCello input
umap = Embeddings(object = Data.Combined, reduction = "umap")
write.table(umap, file="/Users/rbronste/Desktop/VisCello/umap.csv", sep = ",", quote = F, row.names = F, col.names = T)
#If you already computed your dimension reduction result and wants to make a cello for it, use following R code:
cello <- new("Cello", name = "My cell subset", idx = 1:ncol(eset)) # cell_index is which cells from ExpressionSet are used for the dimension reduction
my_umap_proj <- read.table("/Users/rbronste/Desktop/VisCello/umap.csv") # You can put in as many dimension reduction result as you want
cello@proj <- list("My UMAP [2D]" = my_umap_proj) # Put a 2D or 3D in the name to tell VisCello if you want to visualize this as a 2D plot or as a 3D rotatable plot, if 2D there must be 2 columns for each dimension, if 3D there must be 3 columns.
clist <- list()
clist[["Global dataset"]] <- cello
saveRDS(clist, "/Users/rbronste/Desktop/VisCello/clist.rds")
#running VisCello
cello(data_path = "/Users/rbronste/Desktop/VisCello")
I think maybe its something to do with how I am creating a table from the Seurat embedding but Im not sure, any help really appreciated. Thanks.
Sir,how is your VisCello work going ? Have you solved your problem ?
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