Visualize Gene bin score or plot

[TreetoForest]

After studying the GeneTrajectory tutorial and R script in https://klugerlab.github.io/GeneTrajectory/articles/GeneTrajectory.html and github, I successfully completed the entire process.
There are still some confusions that I don’t understand and can’t solve.
Would I discuss this with you？

1. About the “Gene bin score” Visualization
   Question 1 : Where can I get this gene order and expression statues in a ?

The code is bellow:

Gene trajectory inference and visualization

gene_embedding <- GetGeneEmbedding(gene.dist.mat, K = 5)$diffu.emb

Extract 3 gene trajectories

gene_trajectory <- ExtractGeneTrajectory(gene_embedding, gene.dist.mat, N =6, t.list = c(4,7,7), K = 5)
table(gene_trajectory$selected)

pdf("genes.pdf", width = 7, height = 5)

par(mar = c(1.5,1.5,1.5,1.5))
scatter3D(gene_embedding[,1],
gene_embedding[,2],
gene_embedding[,3],
bty = "b2", colvar = as.integer(as.factor(gene_trajectory$selected))-1,
main = "trajectory", pch = 19, cex = 1, theta = 45, phi = 0,
col = ramp.col(c(hue_pal()(3))))

dev.off()

Extract the ordered list of genes along each gene trajectory

gene_list <- list()

for (i in 1:3){
gene_trajectory_sub <- gene_trajectory[which(gene_trajectory$selected == paste0("Trajectory-", i)),]
genes <- rownames(gene_trajectory_sub)[order(gene_trajectory_sub[, paste0("Pseudoorder", i)])]
gene_list[[i]] <- genes
}
str(gene_list)

str(gene_list)
List of 3
$ : chr [1:43] "SASH1" "FCER2" "HLA-DQA2" "HLA-DQA1" ...
$ : chr [1:55] "IFITM3" "MARCKSL1" "PNMA1" "IFIT2" ...
$ : chr [1:153] "PID1" "NR4A1" "CIITA" "INSIG1" ...

str(gene_trajectory )
'data.frame': 251 obs. of 9 variables:
$ DM_1 : num 0.09108 0.06062 -0.00281 0.00107 0.07191 ...
$ DM_2 : num -0.03209 -0.00684 0.0218 0.01764 -0.01563 ...
$ DM_3 : num 0.03116 -0.00252 0.01149 -0.00252 0.00856 ...
$ DM_4 : num -0.06191 0.01476 -0.00406 0.00517 -0.00964 ...
$ DM_5 : num 0.03953 -0.02272 0.01417 0.01583 -0.00482 ...
$ selected : chr "Trajectory-2" "Trajectory-2" "Trajectory-1" "Trajectory-1" ...
$ Pseudoorder1: num 0 0 29 4 0 0 0 20 0 0 ...
$ Pseudoorder2: num 55 42 0 0 46 51 41 0 40 0 ...
$ Pseudoorder3: num 0 0 0 0 0 0 0 0 0 129 ...

Question 2 : How to display it split.by in groups? like in a and c in this figure.

Question 3 : How to analyses it to different Stages status?

2. About the “Gene bin plot” Visualization
   

in e , I have a list of markers of interest like Sox2, they have highers pseudoorder values.

How can I see their trajectory like e , Gene bin-1 to Gene bin -7.
I just want to display the markers of interest.