WebNov 19, 2024 · Value. If do.identify, either a vector of cells selected or the object with selected cells set to the value of identify.ident (if set). Else, if do.hover, a plotly object with interactive graphics.Else, a ggplot object Examples ## Not run: # For functionality analagous to FeaturePlot SpatialPlot(seurat.object, features = "MS4A1") … WebMar 27, 2024 · Seurat can help you find markers that define clusters via differential expression. By default, it identifies positive and negative markers of a single cluster (specified in ident.1 ), compared to all other cells. FindAllMarkers () automates this process for all clusters, but you can also test groups of clusters vs. each other, or against all cells.
How to do subclustering the best? · Issue #4 · vertesy/Seurat…
WebFeb 4, 2024 · # change ident back to Donor data <- SetAllIdent(object = data, id = "Donor") OBS! Each time you want to change colors in a gene plot, you need to change the identity class value in the seurat object in the slot data@ident. Perhaps there is a better way, but I did not find a solution. WebSep 19, 2024 · Error in WhichCells.Seurat (object = x, cells = cells, idents = idents, : Cannot find the following identities in the object: i If I run the last line by itself it works perfectly, namely: immunes.0 <- FindMarkers (AllCells.combined, ident.1 = "VEH", ident.2 = "IMQ", verbose = TRUE, group.by="stim", subset.ident = "0") any advice? thanks! terry glavin national post mass graves
r - Exporting Seurat Object Data by Cluster - Stack Overflow
WebApr 30, 2024 · first how to change the name of orig.ident and how to create a new metadata that combine several orig.ident ex : i have 4 orig.ident : "1", "2", "3", "4" and i would like to create a new metadata to group on one hand "1 and 3" and named it ctrl and on the other hand "2 and 4" and name it patients completed WebApr 30, 2024 · first how to change the name of orig.ident and how to create a new metadata that combine several orig.ident ex : i have 4 orig.ident : "1", "2", "3", "4" and i would like … WebSetIdent: An object with new identity classes set StashIdent: An object with the identities stashed Arguments ... Arguments passed to other methods; for RenameIdents: named … terry glavin ottawa citizen