it is very cool and I wonder if in the new version we can add some downstream analysis function inside

Hi ITALK team,

Thanks for developing such a cool package.
Recently, when I am running the following step with my own data, I got the error:

Error in E<-(*tmp*, value = *vtmp*)

: invalid indexing again and again. Can you help me fix this?

for(comm_type in comm_list){
res_cat<-FindLR(highly_exprs_genes,datatype='mean count',comm_type=comm_type)
res_cat<-res_cat[order(res_cat$cell_from_mean_exprs*res_cat$cell_to_mean_exprs,decreasing=T),]
#plot by ligand category
#overall network plot
NetView(res_cat,col=cell_col,vertex.label.cex=1,arrow.width=1,edge.max.width=5)
#top 20 ligand-receptor pairs
LRPlot(res_cat[1:20,],datatype='mean count',cell_col=cell_col,link.arr.lwd=res_cat$cell_from_mean_exprs[1:20],link.arr.width=res_cat$cell_to_mean_exprs[1:20])
title(comm_type)
res<-rbind(res,res_cat)
}

Many thanks,
Yale

Thanks for this nice tool.

Do you have step-by-step detailed tutorial describing various steps starting from inputing cell-gene expression matrix.

It would make easier to use for beginner like me.

Thank you.

Hello!

I am trying to run DEG function with method="DESeq2" between three groups for single cell RNA seq data.

deg_BcellsM<-DEG(data %>% filter(cell_type=='B-cells-M'),method='DESeq2',contrast=c("grouped_pd","grouped_pr","naive"))
but am getting the following output:

Found more than one class "DataFrame" in cache; using the first, from namespace 'PythonEmbedInR' Also defined by ‘S4Vectors’ Found more than one class "DataFrame" in cache; using the first, from namespace 'PythonEmbedInR' Also defined by ‘S4Vectors’ Found more than one class "DataFrame" in cache; using the first, from namespace 'PythonEmbedInR' Also defined by ‘S4Vectors’ Found more than one class "DataFrame" in cache; using the first, from namespace 'PythonEmbedInR' Also defined by ‘S4Vectors’ Found more than one class "DataFrame" in cache; using the first, from namespace 'PythonEmbedInR' Also defined by ‘S4Vectors’ Found more than one class "DataFrame" in cache; using the first, from namespace 'PythonEmbedInR' Also defined by ‘S4Vectors’ Error in DESeqDataSet(se, design = design, ignoreRank) : some values in assay are not integers

My data file contains the columns as gene names + cell_type and compare_group columns, and the rows are each individual single cell. My groups are named 'grouped_pr', 'grouped_pd', 'naive'.

Do you have any advice on how to proceed?

Thank you!

Hi-- I am trying to use iTALK for my dataset that is in the form of a matrix where gene_names are column headers and individual cells are the row titles.

When I use:
highly_exprs_genes<-rawParse(sseq.data,top_genes=50,stats='mean')
I get the error:
Error in colnames<-(*tmp*, value = c("gene", "exprs", "cell_type")) :
attempt to set 'colnames' on an object with less than two dimensions

Can you please tell me why I am getting this error?

Hi Dear iTALK Teams,

Just wondering how and where you get the information about the class of the gene?
I mean how do you class the ligand genes as a cytokine, checkpoint etc?

Best,
Amare

Hi,

Thanks for creating this great method! I am trying to run DEG for a cell type using:

deg_Mac<-DEG(subset(data, cell_type=='Macrophages'), method='Wilcox', contrast=c("B","A"))

where my two compare_groups are "B" and "A" (data$compare_group). However, I get the following error:

Error in wilcox.test.formula(counts[i, ] ~ groups) : grouping factor must have exactly 2 levels

Appreciate any help!

I have been using this amazing tool for my dataset. I could produce the interaction plot for some dataset without any error. But I'm getting the following error when I used a huge dataset.
Please could you kindly advice how to proceed?

Error: Maybe your gap.degree is too large so that there is no space to
allocate sectors.

str(res)
'data.frame': 3171 obs. of 9 variables:
$ ligand : chr "FN1" "LYZ" "LYZ" "LYZ" ...
$ receptor : chr "CD79A" "ITGAL" "ITGAL" "ITGAL" ...
$ cell_from_logFC : num -2.41 3.34 3.34 3.34 3.34 ...
$ cell_from_q.value: num 0.00408 0.04384 0.04384 0.04384 0.04384 ...
$ cell_from : chr "Stem" "Stromal" "Stromal" "Stromal" ...
$ cell_to_logFC : num 2.1531 0.0001 0.0001 0.0001 0.0001 ...
$ cell_to_q.value : num 7.5e-10 NA NA NA NA ...
$ cell_to : chr "Cycling" "Enterocytes" "InflammationEnterocytes" "T-Cells" ...
$ comm_type : chr "other" "other" "other" "other" ...

Hi.
I have a count dataframe to which I added the cluster information to the cell_type column.
However the DEG function ecaluates length(unique(data$cell_type)) and stops if different than 1. does this mean that I can only have one cell type per data object?

An error message appears after attempting to download the package from Github:

*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘MAST::filter’ by ‘dplyr::filter’ when loading ‘iTALK’
Warning: replacing previous import ‘MAST::combine’ by ‘dplyr::combine’ when loading ‘iTALK’
Warning: replacing previous import ‘dplyr::union’ by ‘igraph::union’ when loading ‘iTALK’
Warning: replacing previous import ‘dplyr::as_data_frame’ by ‘igraph::as_data_frame’ when loading ‘iTALK’
Warning: replacing previous import ‘circlize::degree’ by ‘igraph::degree’ when loading ‘iTALK’
Warning: replacing previous import ‘dplyr::groups’ by ‘igraph::groups’ when loading ‘iTALK’
Warning: replacing previous import ‘igraph::%s%’ by ‘network::%s%’ when loading ‘iTALK’
Warning: replacing previous import ‘igraph::add.edges’ by ‘network::add.edges’ when loading ‘iTALK’
Warning: replacing previous import ‘igraph::get.edge.attribute’ by ‘network::get.edge.attribute’ when loading ‘iTALK’
Warning: replacing previous import ‘igraph::add.vertices’ by ‘network::add.vertices’ when loading ‘iTALK’
Warning: replacing previous import ‘igraph::%c%’ by ‘network::%c%’ when loading ‘iTALK’
Warning: replacing previous import ‘igraph::list.vertex.attributes’ by ‘network::list.vertex.attributes’ when loading ‘iTALK’
Warning: replacing previous import ‘igraph::set.edge.attribute’ by ‘network::set.edge.attribute’ when loading ‘iTALK’
Warning: replacing previous import ‘igraph::is.directed’ by ‘network::is.directed’ when loading ‘iTALK’
Warning: replacing previous import ‘igraph::set.vertex.attribute’ by ‘network::set.vertex.attribute’ when loading ‘iTALK’
Warning: replacing previous import ‘igraph::get.vertex.attribute’ by ‘network::get.vertex.attribute’ when loading ‘iTALK’
Warning: replacing previous import ‘igraph::delete.edges’ by ‘network::delete.edges’ when loading ‘iTALK’
Warning: replacing previous import ‘igraph::is.bipartite’ by ‘network::is.bipartite’ when loading ‘iTALK’
Warning: replacing previous import ‘igraph::get.edges’ by ‘network::get.edges’ when loading ‘iTALK’
Warning: replacing previous import ‘igraph::list.edge.attributes’ by ‘network::list.edge.attributes’ when loading ‘iTALK’
Warning: replacing previous import ‘igraph::delete.vertices’ by ‘network::delete.vertices’ when loading ‘iTALK’
Error: .onLoad failed in loadNamespace() for 'Cairo', details:
call: dyn.load(file, DLLpath = DLLpath, ...)
error: unable to load shared object '/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Cairo/libs/Cairo.so':
dlopen(/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Cairo/libs/Cairo.so, 6): Library not loaded: /opt/X11/lib/libfreetype.6.dylib
Referenced from: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Cairo/libs/Cairo.so
Reason: image not found
Execution halted
ERROR: lazy loading failed for package ‘iTALK’

• removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/iTALK’
  Error: Failed to install 'iTALK' from GitHub:
  (converted from warning) installation of package ‘/var/folders/r3/q936zqs53ml5cbnk24zjb85h0000gp/T//RtmpStGtpm/file39042999453/iTALK_0.1.0.tar.gz’ had non-zero exit status

Hi,
Your work is very impressive, but If I want to highlight the genes with some future (for example, ligands showing insulin signatures), how I am suppose to show in the plot?
Best,
Amare

hi, I used the code to install iTALK nd tried many time but failed, would you help? thanks so much

the code:
devtools::install_github("Coolgenome/iTALK", build_vignettes = TRUE, force = TRUE)

the bug:
`Downloading GitHub repo Coolgenome/iTALK@HEAD
These packages have more recent versions available.
It is recommended to update all of them.
Which would you like to update?

1: All
2: CRAN packages only
3: None
4: slam (0.1-48 -> 0.1-49) [CRAN]

Enter one or more numbers, or an empty line to skip updates: 1
slam (0.1-48 -> 0.1-49) [CRAN]
Installing 1 packages: slam

There is a binary version available but the source version is later:
binary source needs_compilation
slam 0.1-48 0.1-49 TRUE

Do you want to install from sources the package which needs compilation? (Yes/no/cancel) n
trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/slam_0.1-48.tgz'
Content type 'application/x-gzip' length 202614 bytes (197 KB)

downloaded 197 KB

The downloaded binary packages are in
/var/folders/vg/bnpr7f252gvg68_50qt12_z9dxfpv0/T//RtmpsCskTx/downloaded_packages
✓ checking for file ‘/private/var/folders/vg/bnpr7f252gvg68_50qt12_z9dxfpv0/T/RtmpsCskTx/remotes9dfd4e974e05/Coolgenome-iTALK-6d9b390/DESCRIPTION’ ...
─ preparing ‘iTALK’:
✓ checking DESCRIPTION meta-information ...
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
NB: this package now depends on R (>= 3.5.0)
WARNING: Added dependency on R >= 3.5.0 because serialized objects in
serialize/load version 3 cannot be read in older versions of R.
File(s) containing such objects:
‘iTALK/R/sysdata.rda’ ‘iTALK/data/LR_database.rda’
─ building ‘iTALK_0.1.0.tar.gz’
Warning in sprintf(gettext(fmt, domain = domain), ...) :
one argument not used by format 'invalid uid value replaced by that for user 'nobody''
Warning: invalid uid value replaced by that for user 'nobody'
Warning in sprintf(gettext(fmt, domain = domain), ...) :
one argument not used by format 'invalid gid value replaced by that for user 'nobody''
Warning: invalid gid value replaced by that for user 'nobody'

• installing source package ‘iTALK’ ...
  ** using staged installation
  ** R
  ** data
  *** moving datasets to lazyload DB
  ** byte-compile and prepare package for lazy loading
  Warning: replacing previous import ‘Biobase::combine’ by ‘dplyr::combine’ when loading ‘iTALK’
  Warning: replacing previous import ‘dplyr::union’ by ‘igraph::union’ when loading ‘iTALK’
  Warning: replacing previous import ‘dplyr::as_data_frame’ by ‘igraph::as_data_frame’ when loading ‘iTALK’
  Warning: replacing previous import ‘circlize::degree’ by ‘igraph::degree’ when loading ‘iTALK’
  Warning: replacing previous import ‘dplyr::groups’ by ‘igraph::groups’ when loading ‘iTALK’
  Warning: replacing previous import ‘igraph::%s%’ by ‘network::%s%’ when loading ‘iTALK’
  Warning: replacing previous import ‘igraph::add.edges’ by ‘network::add.edges’ when loading ‘iTALK’
  Warning: replacing previous import ‘igraph::get.edge.attribute’ by ‘network::get.edge.attribute’ when loading ‘iTALK’
  Warning: replacing previous import ‘igraph::add.vertices’ by ‘network::add.vertices’ when loading ‘iTALK’
  Warning: replacing previous import ‘igraph::%c%’ by ‘network::%c%’ when loading ‘iTALK’
  Warning: replacing previous import ‘igraph::list.vertex.attributes’ by ‘network::list.vertex.attributes’ when loading ‘iTALK’
  Warning: replacing previous import ‘igraph::set.edge.attribute’ by ‘network::set.edge.attribute’ when loading ‘iTALK’
  Warning: replacing previous import ‘igraph::is.directed’ by ‘network::is.directed’ when loading ‘iTALK’
  Warning: replacing previous import ‘igraph::set.vertex.attribute’ by ‘network::set.vertex.attribute’ when loading ‘iTALK’
  Warning: replacing previous import ‘igraph::get.vertex.attribute’ by ‘network::get.vertex.attribute’ when loading ‘iTALK’
  Warning: replacing previous import ‘igraph::delete.edges’ by ‘network::delete.edges’ when loading ‘iTALK’
  Warning: replacing previous import ‘igraph::is.bipartite’ by ‘network::is.bipartite’ when loading ‘iTALK’
  Warning: replacing previous import ‘igraph::get.edges’ by ‘network::get.edges’ when loading ‘iTALK’
  Warning: replacing previous import ‘igraph::list.edge.attributes’ by ‘network::list.edge.attributes’ when loading ‘iTALK’
  Warning: replacing previous import ‘igraph::delete.vertices’ by ‘network::delete.vertices’ when loading ‘iTALK’
  Warning: replacing previous import ‘igraph::crossing’ by ‘tidyr::crossing’ when loading ‘iTALK’
  ** help
  *** installing help indices
  ** building package indices
  ** testing if installed package can be loaded from temporary location
  Warning: replacing previous import ‘Biobase::combine’ by ‘dplyr::combine’ when loading ‘iTALK’
  Warning: replacing previous import ‘dplyr::union’ by ‘igraph::union’ when loading ‘iTALK’
  Warning: replacing previous import ‘dplyr::as_data_frame’ by ‘igraph::as_data_frame’ when loading ‘iTALK’
  Warning: replacing previous import ‘circlize::degree’ by ‘igraph::degree’ when loading ‘iTALK’
  Warning: replacing previous import ‘dplyr::groups’ by ‘igraph::groups’ when loading ‘iTALK’
  Warning: replacing previous import ‘igraph::%s%’ by ‘network::%s%’ when loading ‘iTALK’
  Warning: replacing previous import ‘igraph::add.edges’ by ‘network::add.edges’ when loading ‘iTALK’
  Warning: replacing previous import ‘igraph::get.edge.attribute’ by ‘network::get.edge.attribute’ when loading ‘iTALK’
  Warning: replacing previous import ‘igraph::add.vertices’ by ‘network::add.vertices’ when loading ‘iTALK’
  Warning: replacing previous import ‘igraph::%c%’ by ‘network::%c%’ when loading ‘iTALK’
  Warning: replacing previous import ‘igraph::list.vertex.attributes’ by ‘network::list.vertex.attributes’ when loading ‘iTALK’
  Warning: replacing previous import ‘igraph::set.edge.attribute’ by ‘network::set.edge.attribute’ when loading ‘iTALK’
  Warning: replacing previous import ‘igraph::is.directed’ by ‘network::is.directed’ when loading ‘iTALK’
  Warning: replacing previous import ‘igraph::set.vertex.attribute’ by ‘network::set.vertex.attribute’ when loading ‘iTALK’
  Warning: replacing previous import ‘igraph::get.vertex.attribute’ by ‘network::get.vertex.attribute’ when loading ‘iTALK’
  Warning: replacing previous import ‘igraph::delete.edges’ by ‘network::delete.edges’ when loading ‘iTALK’
  Warning: replacing previous import ‘igraph::is.bipartite’ by ‘network::is.bipartite’ when loading ‘iTALK’
  Warning: replacing previous import ‘igraph::get.edges’ by ‘network::get.edges’ when loading ‘iTALK’
  Warning: replacing previous import ‘igraph::list.edge.attributes’ by ‘network::list.edge.attributes’ when loading ‘iTALK’
  Warning: replacing previous import ‘igraph::delete.vertices’ by ‘network::delete.vertices’ when loading ‘iTALK’
  Warning: replacing previous import ‘igraph::crossing’ by ‘tidyr::crossing’ when loading ‘iTALK’
  ** testing if installed package can be loaded from final location
  Warning: replacing previous import ‘Biobase::combine’ by ‘dplyr::combine’ when loading ‘iTALK’
  Warning: replacing previous import ‘dplyr::union’ by ‘igraph::union’ when loading ‘iTALK’
  Warning: replacing previous import ‘dplyr::as_data_frame’ by ‘igraph::as_data_frame’ when loading ‘iTALK’
  Warning: replacing previous import ‘circlize::degree’ by ‘igraph::degree’ when loading ‘iTALK’
  Warning: replacing previous import ‘dplyr::groups’ by ‘igraph::groups’ when loading ‘iTALK’
  Warning: replacing previous import ‘igraph::%s%’ by ‘network::%s%’ when loading ‘iTALK’
  Warning: replacing previous import ‘igraph::add.edges’ by ‘network::add.edges’ when loading ‘iTALK’
  Warning: replacing previous import ‘igraph::get.edge.attribute’ by ‘network::get.edge.attribute’ when loading ‘iTALK’
  Warning: replacing previous import ‘igraph::add.vertices’ by ‘network::add.vertices’ when loading ‘iTALK’
  Warning: replacing previous import ‘igraph::%c%’ by ‘network::%c%’ when loading ‘iTALK’
  Warning: replacing previous import ‘igraph::list.vertex.attributes’ by ‘network::list.vertex.attributes’ when loading ‘iTALK’
  Warning: replacing previous import ‘igraph::set.edge.attribute’ by ‘network::set.edge.attribute’ when loading ‘iTALK’
  Warning: replacing previous import ‘igraph::is.directed’ by ‘network::is.directed’ when loading ‘iTALK’
  Warning: replacing previous import ‘igraph::set.vertex.attribute’ by ‘network::set.vertex.attribute’ when loading ‘iTALK’
  Warning: replacing previous import ‘igraph::get.vertex.attribute’ by ‘network::get.vertex.attribute’ when loading ‘iTALK’
  Warning: replacing previous import ‘igraph::delete.edges’ by ‘network::delete.edges’ when loading ‘iTALK’
  Warning: replacing previous import ‘igraph::is.bipartite’ by ‘network::is.bipartite’ when loading ‘iTALK’
  Warning: replacing previous import ‘igraph::get.edges’ by ‘network::get.edges’ when loading ‘iTALK’
  Warning: replacing previous import ‘igraph::list.edge.attributes’ by ‘network::list.edge.attributes’ when loading ‘iTALK’
  Warning: replacing previous import ‘igraph::delete.vertices’ by ‘network::delete.vertices’ when loading ‘iTALK’
  Warning: replacing previous import ‘igraph::crossing’ by ‘tidyr::crossing’ when loading ‘iTALK’
  ** testing if installed package keeps a record of temporary installation path
• DONE (iTALK)

library(iTALK)
Error: package or namespace load failed for ‘iTALK’ in get(method, envir = home):
lazy-load database '/Library/Frameworks/R.framework/Versions/4.1/Resources/library/coin/R/coin.rdb' is corrupt
In addition: There were 23 warnings (use warnings() to see them)`

Hi, I have a SEURAT object that I clustered into 7 clusters,
for the
highly_exprs_genes<-rawParse(Tcells_6,top_genes=50,stats='mean')

I'm getting an error:
Error in [.Seurat(data, data$cell_type == i, ) :
Incorrect number of logical values provided to subset features

The cell_type column contains numbers from 0 to 6 representing each cluster.

Thank you

Hi, the documentation for your DEG function states "Differential expressed genes will
be called within each cell type by the method users select." However, when I run it with data that has more than one cell type, I receive the error message "Error: please compare data with sinlge cell type" How do I generate figures like those found in Figure 2D of the associated bioRxiv paper?
Sweet package by the way, thanks for developing.

Hi! I am trying to use the iTALK package, specifically the code for the example with my data to see how it works.
Could someone help here?:

find the ligand-receptor pairs from highly expressed genes

comm_list <- c("growth factor","other","cytokine","checkpoint")
cell_col<-structure(c("#4a84ad","#4a1dc6","#e874bf","#b79eed", "#ff636b", "#52c63b"),names=unique(data$cell_type))

par(mfrow=c(1,2))
res<-NULL
for(comm_type in comm_list){
res_cat<-FindLR(highly_exprs_genes,datatype='mean count',comm_type="cytokine")
res_cat<-res_cat[order(res_cat$cell_from_mean_exprsres_cat$cell_to_mean_exprs,decreasing=T),]}
res_cat[order(res_cat$cell_from_mean_exprsres_cat$cell_to_mean_exprs,decreasing=T),]

#plot by ligand category
#overall network plot
NetView(res_cat,col=cell_col,vertex.label.cex=1,arrow.width=1,edge.max.width=5)

In the last command (NetView) I get the error: Error in E<-(*tmp*, value = *vtmp*) : invalid indexing

I think the problem must be in the created data file "res_cat" because the description says that it has 0 observations.

it takes a very long time to calculate the DEGS by using DEG() on less than 4000 cells, is there any other method can acerbate this step?

Hello,

I am not sure whether I am just missing anything, but I would like to color the LR links in the chord Plot by the cell of origin.

So for example: I have pulmonary endothelial cells expressing a ligand that is known to interact with receptor in Pericytes. I would like to color that ligands link to the Pericytes by the color given to the endothelial cells. How would I do that?

I have tried to use the same vector as for the cell_col parameter, but that did not work.

Thanks for providing such nice R code! Here i have some questions about the batch effects.
In the reference article (iTALK: an R package to Characterize and Illustrate Intercelluar Communication), it said "iTALK incorporates commonly used algorithms for batch effects corrections and differential gene expression analysis (Online Methods), which also allows the flexibility to select the method that suits the user’s data best." Then i use help("rawParse") function in R, and the document said " Batch information as 'batch' is optional. If included, users may want to use the raw count data for later analysis." When i use "rawParse" function for my own data, i could't find any "batch" related option. I don’t understand how the batch effect is removed in the iTALK package.

Hello,

I get the error below:

Error: Failed to install 'iTALK' from GitHub:
  (converted from warning) unable to access index for repository https://cloud.r-project.org/bin/macosx/el-capitan/contrib/3.5:
  cannot open URL 'https://cloud.r-project.org/bin/macosx/el-capitan/contrib/3.5/PACKAGES'

I tried this on my other computer with R 3.6.2 and got the same error, but .../3.6

Any advice?

Thank you!

Hi!

I think that there's an error in line 577 of your DEG code, specifically using MAST for DEG analysis. You use "valid_cells" before you've created that object. Did you mean "min_valid_cells"?

Really great package though!

Cheers

Erin

Hi!

I found this package spetacular! The main characteristic that draw my attention is the accurate visual illustrations of the LR interactions.

Where can I find more documentation to apply this to my own data? I've found the example to be relatively illustrative, but it still really confusing how to apply this to a user's own data. Besides, running the example script leads to plots that are different from the ones shown in the manuscript.

Are there any further instructions on how to change the labels location so that the network plot may be read and increase plot resolution, just like in the attached manuscript figure? Are there any other categories of LRI other than 'growth factor','other','cytokine' and 'checkpoint' to choose?

I'm eager to merge the analysis done by this package on my data with the rest of my results in order to start to write a manuscript. Any response will be greatly appreciated.

Cheers

How to solve this issue?

table(data2$compare_group)

HNC_TIL Tonsil

3530 5771

deg.genes <- DEG(data2, method='Wilcox', contrast=c("HNC_TIL","Tonsil"))
#Error in DEG(data2, method = "Wilcox", contrast = c("HNC_TIL", "Tonsil")) :

Error: please compare data with sinlge cell type

Hi,
I honestly think that your work very impressive, but I met a problem when I use iTALK R package to process the scRNA-seq data from mice(Mus musculus). It seems that my data can't match the ligand-receptor pairs in your current database probably because the gene names are different between human(upper-case) and mice(lower-case except the first letter).
I'm wondering how to solve this problem and looking forward to your reply.

Hi there,

Thanks for this package, I'm having a lot of fun looking into interactions in my data set! I'm currently having an issues with colors/labels on the Network Plot (see attached image)

In this case, I have my cell_col setup as:
Sensitive_KJ Resistant_KJ
"#00ff00" "#ff0000"

Made from:
cell_col <- structure(c('#00ff00','#ff0000'), names=unique(KJjoined_mat$cell_type))

So that my "Sensitive_KJ" fraction should be green and the other fraction red. These colors and labels are accurately represented in the LR plot, but something goes awry when the network plot works with the same cell_col structure; It inaccurately outputs my sensitive fraction is shown as red! I'm not sure whether I should trust the colors or the labels in this case. Please let me know if you have any suggestions on how to resolve this

Thanks!

cell_col<-structure(c('#f8766d','#d39200','#93aa00','#00ba38','#00c19f','#00b9e3','#619cff','#db72fb','#ff61c3'),names=unique(data$cell_type))

LRPlot(res[1:20,],datatype='mean count',cell_col=cell_col,link.arr.lwd=res$cell_from_mean_exprs[1:20],link.arr.width=res$cell_to_mean_exprs[1:20])

then I got

using cell_col=NULL

is there any option?

Hello!

When plotting the DE genes found with DEG() for multiple subtypes, I receive the following error
`>res_cat<-FindLR(deg_tumor, data_2=c(deg_fibro,deg_tcells), datatype='DEG',comm_type=comm_type)

Error in gene_list_2[, c("gene", "logFC", "q.value", "cell_type")] :
incorrect number of dimensions`

Is it only possible to plot two cell subtypes at a time? The paper example has multiple subtypes.

Thanks!

Dear,
When i perform LRPlot function, i wanna set the track.height_2 = uh(12, "mm"), but turned out
"Error in uh(12, "mm") : could not find function "uh" " I have no idea why this happened.
Hope you can help me with this, really appreciated it!

When I use the fuction FindLR, my result has InF in the logFC. How can I deal with it? Or, what number should I use instead? @ywang65 Thank you !

Hello,

I am trying to run differential expression between Tumor and Tcells LR pairs but am getting
Error: order should contain names of all sectors

I have converted my matrix numeric values to integers (although I received the error before converting as well)

The DEG commands I am running are

deg_Tumor<-DEG(data %>% filter(cell_type=='Tumor'),method='monocle',contrast=c("grouped_pd","grouped_pr")) deg_Tcells<-DEG(data %>% filter(cell_type=='T-cells'),method='monocle',contrast=c("grouped_pd","grouped_pr"))

When I run the for loop line by line I get the above error when running
LRPlot(res_cat_1[1:20,],datatype='DEG',cell_col=cell_col,link.arr.lwd=res_cat$cell_from_logFC[1:20],link.arr.width=res_cat$cell_to_logFC[1:20])

the first comm_type is the "growth factor" and the resulting res_cat matrix has these rows:

Additionally, my DEG objects contain NaNs and -Inf

How does iTALK create these NaNs and NAs? How does iTALK consider the -Infs when running differential expression? Do I need to convert these to a minimum integer value?

Hello, I'm a first time user of the package.
I have an R object, after looking at the example code, I see that the input is a table,
I was wondering how do I go from a SEURAT object to a table to be able to use the package?

data<-read.table('example_data.txt',sep='\t',header=T,stringsAsFactors = F)

Thank you for creating the package!

Hello,

I was hoping you could share more about the input data structure. From the paper and github, it looks like you used a 10X Genomics pbmc dataset, and this 10X data was filtered and normalized in Seurat. What was the code for the data processing in Seurat, as well as how you generated the .txt file from the Seurat data. Thank you! I'm really looking forward to using this program.

Cool package and useful LR pair database!

I can successfully use the FindLR function, etc. for count data but when I input a list of DEGs for various cell types the result is always returned as "No significant pairs found" - even though I can clearly see LR pairs in the data

Im just using the sample code with the following setup (data1 is seen above)

any advice?

Good morning! I am really enjoying trying out your new package! I have 2 questions about some of the output I've been receiving:

1). What are the NAs in the DEG output? How should this be interpreted?

2. I would like to be able to use the DEG results from Seurat in iTALK, so I converted the output FindMarkers in Seurat to a dataframe matching the input columns needed for FindLR, however, I am receiving the following warning message: Can you help me understand what this means?

Thank you very much for your time and help and for making this package!

why i get the plot like below

and here are my code
NetView(iTalk_res,col=cell_col,vertex.label.cex=1,arrow.width=1,edge.max.width=5)

I went over your example_code.r for "highly expressed ligand-receptor pairs", and I am able to successfully visualize that with your package. However I am a little lost on how to get the LRplot for Timepoint 1 vs. Timepoint 2.

I have the data.frame organized into four time points within the format data$time.

Any help would be greatly appreciated.

I honestly think that your work very impressive, i am very interested about classification of L-R database. your article mentioned " based on the known function of the ligand." i want to know where get the function.
i will classify by KEGG, you give me some advice?

Hi, thank you for you excellent work. I am using your R package to find Ligand-receptor interaction in my single cell RNA sequencing data. And I find SPP1-SIPR1 interaction in your dataset, but I wonder if you make a mistake because SGPP1-S1PR1 is correct and there don't exist SPP1-S1PR1 interaction.
Thank you for your attention.

Dear,
This is a really good package, and everything works well. But, i have one question about the LRPlot function. I would like to change the arrow size much smaller by using link.arr.type='big.arrow' , but, nothing arrows coming out at all. I am wondering how to perform this. Thank you very much!