Open moeedakbar opened 4 years ago
Hi,
If I understand well, I think you can use the c.names
argument present in most functions of SingleCellSignalR. cluster
is a numeric vector that attributes each cell to a number (from 1 to max(cluster)
) and c.names
are the names of these clusters (so that length(c.names) = max(cluster)
).
Hope this helps, if not don't hestitate to feed this issue.
Thanks for using SingleCellSignalR,
SCA
Hi @SCA-IRCM ,
I'm a bit confused on how should I specify the c.names
, especially the order.
When I designate cluster
using cluster <- as.numeric(Idents(so))
and check using unique(cluster)
, the output is as below:
unique(cluster)
[1] 1 8 2 14 15 3 11 13 12 7 6 9 10 5 16 4
So when I prepare the c.names
, how should I specify the order? Should I go numerically from 1 to max or follow the unique(cluster)
arrangement?
Hi,
The c.names
argument must go from 1 to max, meaning that the first element of c.names
is the name of the first cluster (cluster = 1), the second element is the name of the second cluster (cluster = 2) and so on.
Hope I'm clear.
Thanks for using SingleCellSignalR.
SCA
Hi, The
c.names
argument must go from 1 to max, meaning that the first element ofc.names
is the name of the first cluster (cluster = 1), the second element is the name of the second cluster (cluster = 2) and so on. Hope I'm clear.Thanks for using SingleCellSignalR.
SCA
Hi, thank you for your prompt reply.
Meaning that if my clusters are as such:
cluster 0 = T cells
cluster 5 = B cells
cluster 4 = Monocytes
cluster 1 = NK cells
cluster 2 = Proliferating cells
cluster 3 = Unknown
my c.names
should be c("T cells", "NK cells", "Proliferating cells", "Unknown", "Monocytes", "B cells")
. The order of the cluster numbers doesn't matter here, am I right? And is it OK to have duplicates cluster names? If not, how can I handle duplicate cell names as some cell clusters are made up of several Seurat clusters.
In addition to that, is it OK if there are dropped numbers in the clusters? For example, I have 22 Seurat clusters, but I subsetted them to remove unwanted cells, so my clusters are missing some numbers and left with 15 clusters. Will that affect the numbering?
Hi,
I confirm that c.names
should be c("T cells", "NK cells", "Proliferating cells", "Unknown", "Monocytes", "B cells")
. Besides, it is not OK to have duplicates in cluster names, I can advise you to iterate the c.names
(for example, T-cells.1, T-cells.2, etc).
Also you need to rescale your cluster vector to avoid holes. I use this type of code:
cluster <- c(1,3,3,2,3,3,2,1,1,5,5,1,5,2,3,5) #there is no cluster 4
cluster[cluster>4)] <- cluster[cluster>4)] - 1
And so on, so that length(c.names)==max(cluster)
.
Hi
I have seurat object, and your package work great!
However, it only lets me find the cluster interactions when the clusters are numeric.
cluster = as.numeric (seuratobject@active.ident). The clusters get rename cluster 1, cluster 2 etc But my clusters are labelled with the cell type, how do I keep those table, ie "Tcells", "macrophages" etc
Many Thanks Moeed