Going through some of the instructions and tutorials for single cell mRNA-Seq analysis, I was looking for some solid and good looking gene expression heatmap plotting following pseudotime, where the gradual shift of transient expression could be clearly shown. Since monocle3 retired the plot_pseudotime_heatmap function, I haven't found any good examples of such function implemented anywhere. Maybe my sources are limited, here are some of the tutorials I've gone through:

broadinstitute.github.io/2019_scWorkshop/functional-pseudotime-analysis.html#plots-of-gene-expression-over-time

scrnaseq-course.cog.sanger.ac.uk/website/biological-analysis.html#expression-of-genes-through-time

satijalab.org/seurat/articles/get_started.html

cole-trapnell-lab.github.io/monocle3/docs/starting/

Do we only have the option to draw such heatmaps by custom code now? In R I could successfully obtain the feature (gene) expression matrix by pseudotime, but I had a hard time to order the features in a good way to show the desired effect of shifting expression through pseudotime, other than the hcluster process applied to the features. If anyone have any good suggestion on this, it would be great!

Here is an example of a similar heatmap. But this is from ArchR and single cell ATAC data. Is there something similar in single cell RNA analysis?

www.archrproject.com/bookdown/images/HemeWalkthrough/PNG/Plot-LymphoidU-Traj-Heatmaps_4.png



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