How to customize the color in 'plot_cell_trajectory' function
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Last seen 15 months ago

Hi, I'm sorry I have a question. I try to color the Module score in the "plotcelltrajectory", here is the codes: data <- AddModuleScore( object =data, features = angio_Features, ctrl = 5, name = 'angio_score', seed = 1 ) #add angio score on each sample

Then I create the monocle object "monocledata", Now I use plotcell_trajectory to check the angio score through pseudotime, the color bar is dark blue to light blue. I want to change the colour.

coul <- colorRampPalette(brewer.pal(8, "RdYlBu"))(25)
  monocle_data, color_by = "angio_score1") + scale_color_manual(breaks = waiver(),values=coul)

Here is the error Error: Continuous value supplied to discrete scale

How can I do this? Thank you.

scRNA seq monocle • 393 views
Entering edit mode
Last seen 3 hours ago
Republic of Ireland

This is more an issue with ggplot2::scale_color_manual more than monocle. What is the waiver() function doing here? Can you please search for the error message ('Error: Continuous value supplied to discrete scale') in order to see how you can fix this problem? - it is a commonly-reported error, but not related to monocle. Coincidentally, there is an example usage of plot_cell_trajectory(..) + scale_color_manual(..) in this Rmd file: Single-cell RNA-seq revealed a concomitant delay in differentiation and cell cycle of aged hematopoietic stem cell



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