Heatmap of genes along pseudotime

[tkapello]

Hi,

I would like to plot a heatmap of the expressed genes along the pseudotime generated by Diffusion Maps. I understand that there is no current function for that, is this correct? Do you have any suggestions?

Theo

[flying-sheep]

Sure! Use pt[cell, ] to get a vector of DPT values starting from cell, then use the order() of those values to reorder your data for the heatmap:

dpt_order <- order(pt[cell, ])
heatmap(data[dpt_order, ])