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aertslab / SCENIC

SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.
http://scenic.aertslab.org
GNU General Public License v3.0
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dotheatmap.R not found when plotRSS(rss) #166

Closed zezhuo closed 2 years ago

zezhuo commented 3 years ago

Hi @s-aibar , Thanks for the nice package. I got a problem when running plotRSS(rss). Attached error messages. Looking forwards to your suggestion.

> rssPlot <- plotRSS(rss)
Showing regulons and cell types with any RSS > 0.01 (dim: 25x7)
Error in file(filename, "r", encoding = encoding) : 
  cannot open the connection
In addition: Warning message:
In file(filename, "r", encoding = encoding) :
  cannot open file '/ddn1/vol1/staging/leuven/stg_00002/lcb/saibar/Projects/aux_scripts/dotheatmap.R': No such file or directory

The other issues that I found are about the memory, multiple cores, and dependencies.

Running out of memory can be solved by reducing cores:

#### Run SCENIC ####
dbs <- c("hg38__refseq-r80__500bp_up_and_100bp_down_tss.mc9nr.feather", "hg38__refseq-r80__10kb_up_and_down_tss.mc9nr.feather")
names(dbs) <- c("500bp", "10kb")
scenicOptions <- initializeScenic(org="hgnc", dbDir="../dbs", dbs = dbs, datasetTitle="chons", nCores=8)

Multiple cores issue of runSCENIC_3 is solved by using one core only.

scenicOptions@settings[["nCores"]] <- 1
scenicOptions <- runSCENIC_3_scoreCells(scenicOptions, exprMat_log)

The following packages are required in my case

#### Load library ####
# Sys.setenv(LANG="en_US.UTF-8")
library(SCENIC)
library(BiocParallel)
library(SCopeLoomR)
library(RColorBrewer)
library(KernSmooth)
library(Seurat)
library(dplyr)

Wish your next updates make the package more friendly to the users.

Regards, Nelson

apaikari commented 3 years ago

cannot open file '/ddn1/vol1/staging/leuven/stg_00002/lcb/saibar/Projects/aux_scripts/dotheatmap.R': No such file or directory

liuyifang commented 3 years ago

same issue Showing regulons and cell types with any RSS > 0.01 (dim: 38x14) cannot open file '/ddn1/vol1/staging/leuven/stg_00002/lcb/saibar/Projects/aux_scripts/dotheatmap.R': No such file or directoryError in file(filename, "r", encoding = encoding) : cannot open the connection

lelesama commented 3 years ago

same issue

vagabond12 commented 3 years ago

same issue

Coke-Zhang commented 3 years ago

Yeah. I have the same error. So how to resolve them ?

Roger-GOAT commented 3 years ago

same issue!!!

Dan-121 commented 2 years ago

I get the same problem,Have any body solve it ?

Dan-121 commented 2 years ago

Guys,I found that we should update the SCENIC devtools::install_github("aertslab/SCENIC",force = TRUE) and the outdate RSQLite is the main reason that make this question