Comments (1)
While not implemented in cellpypes yet, here is code to achieve the same thing:
obj <- seurat %>%
pype_from_seurat() %>%
rule("Tcells", "CD3E", ">", 1) %>%
rule("Treg", "FOXP3", ">", .1, parent="Tcells") %>%
rule("Treg_eff","ICOS", ">", 1.5, parent="Treg") %>%
rule("Treg_mem","CCR7", ">", 1.5, parent="Treg")
# replace clusters 4,5 and 7 with cellpype labels:
pype_types <- as.character(classify(obj, c("Treg_eff", "Treg_mem")))
clusters <- as.character(seurat$seurat_clusters)
seurat$edited_clusters <- case_when(
clusters %in% c(4,5,7) ~ pype_types,
TRUE ~ clusters)
# plot result:
DimPlot(seurat, group.by = "edited_clusters")
from cellpypes.
Related Issues (20)
- embedding instead of embed
- precompute function HOT 2
- plot_last function HOT 1
- dot_plot function
- parent invalid gives unclear error message
- plot_classes/classify: Handle overlap between parent and child HOT 1
- plot_last: make plots the same size HOT 1
- pype_from_seurat only works on simple cases HOT 1
- cellpypes does not handle objects processed with SoupX HOT 1
- threshold in rule function HOT 6
- Genes in rows (not columns) HOT 1
- Backtrace which cells that got classified? HOT 5
- pype_from_seurat function HOT 3
- options function for cellpypes HOT 1
- class_factor function and class_matrix function HOT 1
- plot_overlap function
- Function to combine objects
- Function: group_classes (OR logic for rules) HOT 4
- format_rules function HOT 1
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from cellpypes.