Comments (8)
Hi @natalkon , I just updated the package to support such action. You can re-label cells without re-doing computeCommunProb
from cellchat.
Dear @sqjin ,
I tried to update the package simply by
devtools::install_github("sqjin/CellChat")
But I got
Error: Failed to install 'CellChat' from GitHub:
(converted from warning) installation of package ‘backports’ had non-zero exit status
How can I overcome it?
Thanks!
from cellchat.
Dear @sqjin ,
I have manually deleted the "backports" folder from the library, downloaded the package "backports_1.1.9.zip" from CRAN https://cran.r-project.org/web/packages/backports/index.html and placed the new "backports" into the library.
After that updating the package with
devtools::install_github("sqjin/NMF")
devtools::install_github("sqjin/CellChat")
was no problem.
But after
identity = data.frame(group = sc_data$cell_type, row.names = names(sc_data$cell_type)) # create a dataframe consisting of the cell labels
unique(identity$group)
cellchat <- addMeta(cellchat, meta = identity, meta.name = "cell_type")
cellchat <- setIdent(cellchat, ident.use = "cell_type") # set "cell_type" as default cell identity
levels(cellchat@idents)
groupSize <- as.numeric(table(cellchat@idents))
Re-labelling worked for
CellChat::netVisual_aggregate(cellchat, signaling = c("TGFb"), layout = "circle", vertex.size = groupSize)
but still did not happen in
CellChat::netAnalysis_river(cellchat, pattern = "outgoing")
or in
CellChat::netAnalysis_dot(cellchat, pattern = "outgoing")
Do you know what could be the reason for that?
Thanks!
from cellchat.
@natalkon As I mentioned that "You can re-label cells without re-doing computeCommunProb", thus you need to re-run all the functions after computeCommunProb
.
from cellchat.
@sqjin That is amazing! Thank you!!!
from cellchat.
@sqjin
Hi, I tried to change one label in both the metadata and idents:
levels(cellchat@meta$labels)[levels(cellchat@meta$labels) =='Mast cells' ] <- 'Mc 4'
levels(cellchat@idents)[levels(cellchat@idents) =='Mast cells' ] <- 'Mc 4'
table(cellchat@idents)
The label was changed successfuly.
And then I run the code after computeCommunProb
, but when I try to plot, the label is still 'Mast cells', even for the CellChat::netVisual_aggregate
function.
Could you please give advice?
Thanks!
from cellchat.
Hi @ruohuchengxhe , you should do it levels(cellchat@meta$labels)[levels(cellchat@meta$labels) =='Mast cells' ] <- 'Mc 4' cellchat <- setIdent(cellchat, ident.use = "cell_type") # set "cell_type" as default cell identity
from cellchat.
Hi @ruohuchengxhe , you should do it
levels(cellchat@meta$labels)[levels(cellchat@meta$labels) =='Mast cells' ] <- 'Mc 4' cellchat <- setIdent(cellchat, ident.use = "cell_type") # set "cell_type" as default cell identity
Sure! Didn't do this. Thanks!
from cellchat.
Related Issues (20)
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from cellchat.