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sctalk's Introduction

scTalk

scTalk is an R package for intercellular communication (ligand-receptor) analysis from scRNA-seq data and implements the method described in Farbehi et al.. Please read the vignette for an explanation of how to use the software.

Installation

To install scTalk, open an R session and use the following commands:

install.packages("devtools")
devtools::install_github("VCCRI/scTalk", build = TRUE, build_vignettes = TRUE, build_opts = c("--no-resave-data", "--no-manual"))

To access the vignette:

library(scTalk)
browseVignettes("scTalk")

Citation

If you find scTalk useful in your research, please cite the following paper:

Farbehi N, Patrick R, Dorison A, Xaymardan M, Janbandhu V, Wystub-Lis K, Ho JWK, Nordon RE, and Harvey RP. Single-cell expression profiling reveals dynamic flux of cardiac stromal, vascular and immune cells in health and injury. eLife, 8:e43882, 2019.

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sctalk's Issues

error in generating circleplot

Hi all!

Sorry to raise issues again, I have been working thru the vignette using my own dataset and have been able to generate significant cell-cell interaction in table format. However, when I try to generate a circle plot using the follow code, I get an error:

> cell.network.file = paste0("Permutation_tests_", file.lab, "_network.csv")
> CellCirclePlot(input.file = cell.network.file, 
+                adj_pval_thresh = 0.01)
Error in (function (edges, n = max(edges), directed = TRUE)  : 
  At structure_generators.c:86 : Invalid (negative) vertex id, Invalid vertex id

I have reviewed my result.table, etc. and they seem to be expected. What does this error mean?

Thanks,
Wei

String database question

Hi guys! Quick question on the string reference. Does it compare my data to all available string annotations? How can I compare only to experimentally validated annotations?

Thanks,
Wei

Error with EvaluateConnections

Hi, thanks for the nice package, I just want to ask what is the difference between the populations.use argument and pct.threshold argument in the GenerateEdgeWeights() function?

Also, since I have to run the workflow a lot of times across different combinations I've been trying to run the EvaluateConnections() with different populations.use however I'm getting these errors how can I solve them?

Error in { : 
  task 2 failed - "cannot take a sample larger than the population when 'replace = FALSE'"
In addition: Warning message:
In e$fun(obj, substitute(ex), parent.frame(), e$data) :
  already exporting variable(s): complete.path.table, background.table

another error with GenerateEdgeWeights

Hi Ralph and colleagues,

I am encountering a new error with GenerateEdgeWeights() while applying it to a new dataset published on COVID PMBCs by the Blish group.

Here is what I see,

> populations.use <- names([email protected][["SingleR.calls"]]) #i used singleR's annotation here
> ## Define a label for output files
> file.lab <- "TIP"

> GenerateEdgeWeights(seurat.object = blish,
+                     file.label = file.lab, # output file
+                     species = "human",
+                     populations.use = populations.use,
+                     string.ver = "11.0",
+                     verbose = TRUE) # this is a bug, need to run this line
[1] "Calculating cluster-specific ligand/expression characteristics"
Error in apply(expression.matrix[, cell.set], 1, function(x) { : 
  dim(X) must have a positive length

I rechecked and this operation worked on my previous dataset. I am not sure what the error means,

Wei

CellCirclePlot title

Hello all!

I'm using scTalk a lot lately and I was wondering what is the correct way to add a title to a CellCirclePlot. I have tried with the base main parameter as well as ggplot's labs(title = "my title") but none of them seem to work.

Could you help with this?

Thanks a lot!

Paula

STRINGdb error while running GenerateEdgeWeights()

Hello!

I have a preprocessed Seurat object that I passed into GenerateEdgeWeights(). Here is my code:

populations.use <- names(table(Idents(stanford)))
## Define a label for output files
file.lab <- "TIP"
GenerateEdgeWeights(seurat.object = stanford,
                    file.label = file.lab, # output file
                    species = "human",
                    populations.use = populations.use)

Where 'stanford' is my seurat object. However, I am receiving this following output:

> GenerateEdgeWeights(seurat.object = stanford,
+                     file.label = file.lab, # output file
+                     species = "human",
+                     populations.use = populations.use)
[1] "Calculating cluster-specific ligand/expression characteristics"
[1] "Identifying all potential cluster:ligand:receptor:cluster paths"
ERROR: Currently STRINGdb only supports the most recent version of STRING:  11.0Error in .Object$initialize(...) :

I am not sure how to proceed, could you please advise?
Thank you!
Wei

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