Replying to my own message above, the R code can be found in the publication :

"https://pubmed.ncbi.nlm.nih.gov/32094115/"

https://github.com/crickbabs/ZebrafishDevelopingHindbrainAtlas

and the lines or R code that are relevant are :

```
genes <- read.delim("data/TF_heatmap.txt",header=T,sep="\t",stringsAsFactors=F)[,2]
pt.matrix <- as.matrix(cds@assays$data$counts[match(genes,rowData(cds)[,2]),order(pseudotime(cds))])
pt.matrix <- t(apply(pt.matrix,1,function(x){smooth.spline(x,df=3)$y}))
pt.matrix <- t(apply(pt.matrix,1,function(x){(x-mean(x))/sd(x)}))
rownames(pt.matrix) <- genes;
ht <- Heatmap(
pt.matrix,
name = "z-score",
col = colorRamp2(seq(from=-2,to=2,length=11),rev(brewer.pal(11, "Spectral"))),
show_row_names = TRUE,
show_column_names = FALSE,
row_names_gp = gpar(fontsize = 6),
km = 6,
row_title_rot = 0,
cluster_rows = TRUE,
cluster_row_slices = FALSE,
cluster_columns = FALSE)
print(ht)
```