VisCello Shiny app code for hosting snRNA-seq data
0
0
Entering edit mode
15 months ago
LacquerHed ▴ 20

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.

shiny scRNA-seq snRNA-seq VisCello • 660 views
ADD COMMENT
0
Entering edit mode

Sir,how is your VisCello work going ? Have you solved your problem ?

ADD REPLY
0
Entering edit mode

Please do not add an answer unless you're answering the top level question. Use Add Comment or Add Reply instead as appropriate. I've moved your post to a comment this time, but please be more careful in the future.

ADD REPLY

Login before adding your answer.

Traffic: 1425 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6