When I run following code, I get error at -
slingshot_df <- data.frame(colData(sce))
the error is :
Error in as.vector(x) : no method for coercing this S4 class to a vector
library(Polychrome)
library(ggbeeswarm)
library(ggthemes)
# this define the cluster color. You can change it with different color scheme.
my_color <- createPalette(length(levels(sce$ident)), c("#010101", "#ff0000"), M=1000)
names(my_color) <- unique(as.character(sce$ident))
slingshot_df <- data.frame(colData(sce))
# re-order y-axis for better figure: This should be tailored with your own cluster names
# slingshot_df$ident = factor(slingshot_df$ident, levels=c(4,2,1,0,3,5,6))
ggplot(slingshot_df, aes(x = slingPseudotime_1, y = ident,
colour = ident)) +
geom_quasirandom(groupOnX = FALSE) + theme_classic() +
xlab("First Slingshot pseudotime") + ylab("cell type") +
ggtitle("Cells ordered by Slingshot pseudotime")+scale_colour_manual(values = my_color)