how I can add the pseudotime metadata information to other package such as TSCAN to do pseudotime plot？

[Sophia409]

@rcannood @Xiaojieqiu Hello,thank you for your work. First ,I have to say tha I have compared the both methods to do pseodotime analysis.One is by importing Seurat batch corrected integrated data to monocle,the other is to use orinal expression data to monocle and do batch corrected through the fuction fullModelFormulaStr. But it's obvious that the result that ordered by Seurat corrected data（the first picture）is much better and conform to reality.The trajectory orderred by fullModelFormulaStr corrected data is non-ideal(the second picture). But it's really a shame that if I use Seurat batch corrected data to ordercells,I can't get gene expression dynamic picture,including genes_branched_pseudotime and genes_branched_heatmap.So I'm wondering if I can extract pseudotime coordinates from pData(or named metadata,and export it to other package to do these plots.I can add the pseudotime metadata information to Seurat object which has tha original expression data),but this package can't be used to do pseudotime plot. Can you add other better batch corrected method to monocle2,such as Mnn corrected?Or can you add two assay to monocle object?Or do you have any idea that how I can add the pseudotime metadata information to other package such as TSCAN to do pseudotime plot？ I'm really confused and troubled.Hope your help.

[Dragonmasterx87]

I see that there is no resolution of this as yet :(