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Error in `E<-`(`*tmp*`, value = `*vtmp*`) : invalid indexing #9

Open Yale73 opened 4 years ago

Yale73 commented 4 years ago

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

BoadiceaCc commented 4 years ago

Hi, I get the exact same problem here, using the same code from iTALK package but with my own data.

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

Did you find the solution, or does anyone knows how to help? Thank you much,

Edit: I actually just found my mistake.

comm_type : Communication type. Available options are "cytokine", "checkpoint", "growth factor", "other". I just replaced comm_type = comm_type in the FindLR function with the categories

ywang65 commented 4 years ago

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

Examples here are just showing how to use these functions. If you test dim(res_cat), it will be 0. And this is the reason why there is an error