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


# 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)


Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Browse other questions tagged or ask your own question.