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Colour_Scheme.R
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# Function to get the same colours as used by default in Seurat DimPlot
get_seurat_colours <- function(obj, group.by) {
require(scales)
identities <- obj@meta.data[,group.by]
if (class(identities) != "factor") {
identities <- factor(identities)
}
identities <- levels(identities)
my_color_palette <- hue_pal()(length(identities))
return(my_color_palette)
#usage:
# TSNEPlot(object = object, do.return = T) +
# scale_color_manual(values = my_color_palette)
}
## Map Subtypes to general cell-type labels ##
simplify_annotations <- function(annotations, types=c("B", "Mac", "T", "Hep")) {
simplified <- as.character(annotations)
if ("B" %in% types) {
simplified[simplified %in% c(
"AntibodysecretingBcells",
"MatureBcells", "B_cells", "any_B_cell", "Anti_B")] <- "Bcells"
}
if ("Mac" %in% types) {
simplified[simplified %in% c(
"InflamatoryMacrophages", "Non-inflammatoryMacrophages")] <- "Macrophages"
}
if ("T" %in% types) {
simplified[simplified %in% c(
"CD3abTcells", "gdTcells1", "gdTcells2", "gd_T_1", "gd_T_2", "CD3_T")] <- "Tcells"
}
if ("Hep" %in% types) {
simplified[simplified %in% c(
"PericentralHep", "UnidentifiedHep", "PeriportalHep",
"interzonalHep", "Hep", "PortalHep2", "PortaHep1", "PortHep", "CentralHep1", "CentralHep")] <- "Hepatocyte"
}
return(simplified);
}
Cell_type_colours <- rbind(
c("ambiguous", "#7F7F7F"), #grey50
c("Eryth", "#8B0000"), #darkred
c("Hepatocyte", "#e41a1c"), #bright red
c("OtherHep", "#e41a1c"), #bright red
c("PortalHep", "#084081"),
c("interHep", "#0868ac"),
c("CentralHep", "#2b8cbe"),
c("Stellate", "#fec44f"),
c("Cholangiocyte", "#ec7014"),
c("Portalendo", "#993494"),
c("Macrophage", "#377eb8"), # bright blue
c("NonInfMac", "#377eb8"),
c("InfMac", "#41b6c4"),
c("Tcell", "#4daf4a"), #green
c("gdTcells1", "#41ae76"),
c("gdTcells2", "#00441b"),
c("CD3abTcells", "#4daf4a"),
c("Bcell", "#f781bf"), #violet
c("AntiBcell", "#f78abf"), #violet
c("MatBcell", "#6a51a3"), #violet
c("NKcells", "#a65628"),
c("LSECs", "#ffff33"),
c("cvLSECs", "#ff7f00"),
c("PortalLSECs", "#4d004b"))
colnames(Cell_type_colours) <- c("type", "colour")
map_cell_types <- function(types) {
type <- as.character(types)
tab <- unique(matrix(c("ambiguous", "ambiguous",
"None", "ambiguous",
"AntibodysecretingBcells", "AntiBcell",
"AntiBcell", "AntiBcell",
"Bcells", "Bcell",
"B_cells", "Bcell",
"any_B_cell", "Bcell",
"Bcell", "Bcell",
"CD3abTcells", "CD3abTcells",
"CD3abTcell", "CD3abTcells",
"NaiveTcell", "CD3abTcells",
"CentralvenousLSECs", "cvLSECs",
"CV_LSECs", "cvLSECs",
"cvLSECs", "cvLSECs",
"cvLSEC", "cvLSECs",
"LSECs", "LSECs",
"Cholangiocytes", "Cholangiocyte",
"Cholangiocyte", "Cholangiocyte",
"Cholan", "Cholangiocyte",
"Chol", "Cholangiocyte",
"Erythoidcells", "Eryth",
"Erythoid", "Eryth",
"Erythroid", "Eryth",
"Erythroidcells", "Eryth",
"Eryth", "Eryth",
"gdTcells1", "gdTcells1",
"gd_T_1", "gdTcells1",
"gd_T_2", "gdTcells2",
"gdTcell", "gdTcells2",
"Hepatocyte", "Hepatocyte",
"Hepatocytes", "Hepatocyte",
"Hep", "Hepatocyte",
"inflamatoryMacrophages", "InfMac",
"InflamatoryMacrophages", "InfMac",
"InflammatoryMacrophages", "InfMac",
"inflammatoryMacrophages", "InfMac",
"InfMac", "InfMac",
"Infl_Mac", "InfMac",
"interzonalHep", "interHep",
"interHep", "interHep",
"InterHep", "interHep",
"Macrophage", "Macrophage",
"Mac", "Macrophage",
"Macrophages", "Macrophage",
"MatureBcells", "MatBcell",
"MatBcell", "MatBcell",
"NK-likecells", "NKcells",
"NK_like", "NKcells",
"NKTcell", "NKcells",
"NKTcells", "NKcells",
"NKcells", "NKcells",
"Non-inflammatoryMacrophages", "NonInfMac",
"NonInfl_Mac", "NonInfMac",
"NonInflMac1", "NonInfMac",
"NonInflMac22", "NonInfMac",
"NonInfMac", "NonInfMac",
"PericentralHep", "CentralHep",
"CentralHep", "CentralHep",
"CentralHep1", "CentralHep",
"PeriportalHep", "PortalHep",
"PortaHep1", "PortalHep",
"PortaHep2", "PortalHep",
"PortalHep2", "PortalHep",
"PortalHep1", "PortalHep",
"PortalHep", "PortalHep",
"PortHep", "PortalHep",
"PeriportalLSECs", "PortalLSECs",
"PeriLSECs", "PortalLSECs",
"PortalLSECs", "PortalLSECs",
"pLSECs", "PortalLSECs",
"pLSEC", "PortalLSECs",
"PortLSECs", "PortalLSECs",
"Periportalendothelialcells", "Portalendo",
"Portal_Endo", "Portalendo",
"PortalEndo", "Portalendo",
"Portal_Endo", "Portalendo",
"PortEndo", "Portalendo",
"Portalendothelialcells", "Portalendo",
"Portalendo", "Portalendo",
"Stellatecells", "Stellate",
"Stellate", "Stellate",
"Tcell", "Tcell",
"Tcells", "Tcell",
"gdTcells2", "gdTcells2",
"UnidentifiedHep", "OtherHep",
"OtherHep", "OtherHep",
"Bcell", "Bcell",
"Cholan", "Cholangiocyte",
"PortHep", "PortalHep",
"Anti_B", "AntiBcell",
"any_B_cell", "Bcell",
"any_T_cell", "Tcell",
"B_cells", "Bcell",
"CD3_T", "CD3abTcells",
"Bcells", "Bcell"), ncol=2, byrow=TRUE))
colnames(tab) <- c("orig", "tidy");
return(tab[match(types,tab[,1]),2])
}
type_2_colour <- function(type) {
type <- as.character(map_cell_types(type))
colour <- Cell_type_colours[match(type, Cell_type_colours[,"type"]),"colour"]
return(colour)
}
Type_DimPlot <- function(myseur, type_col="consistent_labs", reduction="umap", cluster_col="seurat_clusters") {
require(ggplot2)
agg_coord_by_cluster <- function(coords, clusters) {
x <- split(seq(nrow(coords)), clusters)
result <- sapply(x, function(a) apply(coords[a,],2,median))
return(result)
}
umap_lab_pos <- agg_coord_by_cluster(Reductions(myseur, reduction)@cell.embeddings, myseur@meta.data[,cluster_col])
# UMAP + Ref scmap anno
new_colour_scheme <- Cell_type_colours[order(Cell_type_colours[,1]),]
myseur@meta.data[,type_col] <- map_cell_types(myseur@meta.data[,type_col])
new_colour_scheme <- new_colour_scheme[new_colour_scheme[,1] %in% myseur@meta.data[,type_col],]
DimPlot(myseur, reduction=reduction, group.by=type_col, pt.size=.1)+scale_color_manual(values=new_colour_scheme[,2])+annotate("text", x=umap_lab_pos[1,], y=umap_lab_pos[2,], label=colnames(umap_lab_pos), colour="grey35")
}