dibbelab/gficf

An R implementation of the Gene Frequency - Inverse Cell Frequency method for single cell data normalization

gficf's Issues

An error occurred while running the runScGSEA

Hello!

Thanks to your package, I'm proceeding with scGSEA with my single-cell RNA seq data.
But I faced a problem.
I keep getting this error while I'm running this code.

What methods do you recommend to solve this problem?
I need your help.
Thank you!

Here's the code I ran.

library(gficf)
library(ggplot2)
library(Seurat)
library(dplyr)

data <- gficf( M = Control.data)
data <- runPCA(data = data,dim = 30,use.odgenes = T)
data <-runReduction(data = data,reduction = "umap",nt = 2,verbose = T,n_neighbors=150)
p = plotCells(data = data) +  xlab("UMAP 1") +  ylab("UMAP 2")
plot(p1)

data <-  runScGSEA(data = data ,
                 geneID = "ensamble",
                 species = "mouse",
                 category = "H",
                 fdr.th = 0.05,
                 nmf.k = 50,
                 rescale = "none",
                 verbose = T)

15:58:22 ... Performing NMF
Error in RcppML::nmf(data = data$gficf, k = nmf.k) : 
  unused argument (data = data$gficf)

15:58:22 ... Performing NMF
Error in RcppML::nmf(data = data$gficf, k = nmf.k) :
unused argument (data = data$gficf)

object '_gficf_rcpp_parallel_jaccard_coef' not found in clustcells()

Hello,

I'm currently using the clustcells() function for clustering, but I'm running into issues with the rcpp parts of the function. I'm currently on mac and I have followed the installation instructions on the main page. Is there another package that I'm missing?

Rphenograph.out <- clustcells(data = as.matrix(fcs.data.heat), nt = 12 ,k = 30)
Finding Neighboors..TRUE
Found more than one class "dist" in cache; using the first, from namespace 'BiocGenerics'
Also defined by ‘spam’
00:23:00 Building Annoy index with metric = manhattan, n_trees = 50
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
00:23:52 Writing NN index file to temp file /var/folders/tw/p_th3mmn3hl7_cl89xq8z4yr0000gs/T//RtmpMawIF1/file13709758a7b4d
00:23:53 Searching Annoy index using 12 threads, search_k = 3100
00:24:24 Annoy recall = 100%
Error in rcpp_parallel_jaccard_coef(neigh, verbose) :
object '_gficf_rcpp_parallel_jaccard_coef' not found

Edit: I thought I sourced the new functions somewhere (https://rdrr.io/github/dibbelab/gficf/src/R/RcppExports.R), but I don't think I did this correctly. A resource for anyone else who needs to bind the packages - https://rdrr.io/rforge/Rcpp/man/compileAttributes.html.

Merge multiple gficf objects

Hi,
Can you suggest how to run gficf for multiple samples?
I ran gficf on individual samples, is there a way to merge them together and then run scGSEA?

Can I Performing scGSEA by using Seurat object?

In tutorial, program looks like start from RAW counts matrix.
Can I use normalized Seurat object which have already done PCA UMAP?

data("small_BC_atlas")

data <- gficf( M = small_BC_atlas)

data <- runPCA(data = data,dim = 10,use.odgenes = T)

data <-runReduction(data = data,reduction = "umap",nt = 2,verbose = T,n_neighbors=150)

Can't install gficf v2

g++ -shared -s -static-libgcc -o gficf.dll tmp.def ModularityOptimizer.o RModularityOptimizer.o RcppExports.o detectCores.o jaccard_coeff.o mann_whitney.o misc.o rcpp_mann_whitney.o rcpp_parallel_jaccard_coeff.o rcpp_parallel_mann_whitney.o -L/lib/x64 -lgsl -lgslcblas -LC:/Users/jianj/AppData/Local/R/win-library/4.3/RcppParallel/lib/x64 -ltbb -ltbbmalloc -fopenmp -LC:/RBuildTools/4.3/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/RBuildTools/4.3/x86_64-w64-mingw32.static.posix/lib -LC:/PROGRA1/R/R-431.0/bin/x64 -lR
C:\RBuildTools\4.3\x86_64-w64-mingw32.static.posix\bin/ld.exe: misc.o:misc.cpp:(.text.hot+0x1c5): undefined reference to dgemm_' C:\RBuildTools\4.3\x86_64-w64-mingw32.static.posix\bin/ld.exe: misc.o:misc.cpp:(.text.hot+0x2aa): undefined reference to dgemv_'
C:\RBuildTools\4.3\x86_64-w64-mingw32.static.posix\bin/ld.exe: misc.o:misc.cpp:(.text.hot+0x607): undefined reference to `dsyrk_'
collect2.exe: error: ld returned 1 exit status
no DLL was created
ERROR: compilation failed for package 'gficf'

Error installing github version on windows10

Hi,

I had some issues installing the github version. The problem seemed to be that the gsl libraries were incompatible. Possibly a 32bit issue?
I followed this guide
https://stackoverflow.com/questions/23640088/setting-up-rcpp-gsl-for-windows/23666023#23666023
but using local323.zip instead of local300.zip, exporting it and then running
Sys.setenv(GSL_LIBS = '"C:/Program Files/R/local323"')
before installation seemed to do the trick.

error on installing 'netbiov' package

Hello,

When I was running the tutorial scripts for 'Single-cell Gene Set Enrichement Analysis', I got an error message from running, 'BiocManager::install("netbiov")' as below;

---

BiocManager::install("netbiov")
'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
CRAN: https://cloud.r-project.org
Bioconductor version 3.18 (BiocManager 1.30.22), R 4.3.2 (2023-10-31)
Installing package(s) 'netbiov'
Installation paths not writeable, unable to update packages
path: /usr/lib/R/library
packages:
boot, cluster, mgcv, nlme
path: /usr/lib/R/site-library
packages:
cli, desc, isoband, matrixStats, pkgbuild, processx, QuickJSR, svglite
Warning message:
package 'netbiov' is not available for Bioconductor version '3.18'

A version of this package for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages

So, could you please help me install the package to do plotting the network?

Best regards,

Jinhong

data("small_BC_atlas") doesnt seem to work

Dear developers,

thanks for the great package. I'm excited to try it but I'm not able to load the example dataset.
I get this error when I try to load.

library(gficf)
data("small_BC_atlas")

Warning message:
In data("small_BC_atlas") : data set ‘small_BC_atlas’ not found

Error in readRDS

Hi, I am also running DREEP using the sample data which needs well installion of gficf; however, it turns out as follows. Could anyone help? Thanks a lot!

data(small_BC_atlas)
data <- gficf(M=small_BC_atlas,verbose = T)
09:36:00 Gene filtering..
09:36:05 Normalize counts..
09:36:26 Apply GF transformation..
09:36:27 Compute ICF weigth..
09:36:27 Applay ICF..
09:36:28 Apply l2
dreep.data <- DREEP::runDREEP(M = data$gficf,n.markers = 250, gsea = "multilevel",gpds.signatures = c("CTRP2","GDSC"))
09:37:02 Loading GPDS signatures..
Error in readRDS(paste0(find.package("DREEP"), "/data/", i, ".gpds.rds")) :
unknown input format