Exporting gene list ordered by trajectory

[LacquerHed]

Hi I have run the following and would like to export a gene list based on trajectory ordering for the heatmap, just not sure how to how to go about that since the SummarizedExperiment is not a ranked list? Thanks!

#Similarly, we can obtain a pseudo-time heatmap of gene expression by setting useMatrix = "GeneIntegrationMatrix"
trajGIM <- getTrajectory(ArchRProj = NTS_PEC_ArchR_subset_C9_integrated1, name = "PEC", useMatrix = "GeneIntegrationMatrix", log2Norm = FALSE)
p3 <- plotTrajectoryHeatmap(trajGIM,  pal = paletteContinuous(set = "blueYellow"))
p3

[LacquerHed]

Any ideas on this? Thanks!

[rcorces]

Sorry - I have been traveling.
The object returned by plotTrajectoryHeatmap() is just a ComplexHeatmap object. As such, you can inspect that object to retrieve all of the data stored in the heatmap.

> trajGSM <- getTrajectory(ArchRProj = projHeme5, name = "MyeloidU", useMatrix = "GeneScoreMatrix", log2Norm = TRUE)
> p2 <- plotTrajectoryHeatmap(trajGSM,  pal = paletteContinuous(set = "horizonExtra"))
> head(p2@ht_list$GeneScoreMatrix@row_names_param$labels)
[1] "chr3:MIR5193"  "chr16:ZNF423"  "chr19:MIMT1"   "chr19:MIR320E"
[5] "chr22:SYN3"    "chr17:SPNS2"