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Y-axis of plot_genes_in_pseudotime #534

Open TsukasaKo opened 2 years ago

TsukasaKo commented 2 years ago

Dear all, I would like to run monocle3 package with Seurat integrated data.

For this I used below command. library(SeuratWrappers) library(monocle3) library(monocle)

pbmc3.cds <- as.cell_data_set(x) cds <- preprocess_cds(pbmc3.cds, num_dim = 50) colData(cds)$cell_type_seurat <- x@meta.data$cluster_name cds <- reduce_dimension(cds) cds <- cluster_cells(cds) cds <- learn_graph(cds) cds@clusters$UMAP$partitions[cds@clusters$UMAP$partitions == "2"] <- "1" cds <- learn_graph(cds, use_partition = F)

Pseudotime plot looks reasonable. However value they have, I have no idea. What is % Max in legend ? Rplot01

Also I did plot_genes_in_pseudotime, however I got such plots, which is no make sense for expression, Rplot02

I wonder why expression is not reflected while exprs(cds) has expression value. If used as.cell_data_set, this error would be happened ? Thanks,

ctlshcxy commented 2 years ago

Hi, I met the same problem like you, have you solved this problem?

lixining2020 commented 2 years ago

I have the same issue, just wonder whether you have solved yet or any suggestions? Thanks~

vagabond12 commented 2 years ago

Hi, I have the same issue, and I hope someone could help us solve this problem, Thank you.