Hi,
Thank you for developing this awesome tool!
I notice that when I choose what clusters to display on the UMAP, the scale on the axes changes accordingly. Is there a way to have a fixed scale? Thanks!

Hi guys! could some one give me tips on how to save 3D-UMAP in a movie for power point presentation purposes?

Line 44: The name of the dataframe needs to consistent. I assume this was a typo!
Keep it either plotting.data or plot.data

Hello,
When I ran the 3d umap for seurat encounter following error. Did anyone find how to work it out? Thanks.

Code:

goi <- "TOP2A"
plotting.data <- FetchData(object = yourseuratobject, vars = c("UMAP_1", "UMAP_2", "UMAP_3", "Expression"=goi), slot = 'data')
Warning message:
In FetchData(object = yourseuratobject, vars = c("UMAP_1", "UMAP_2", :
The following requested variables were not found: TOP2A

Code is very helpful; thank you!

Not an 'issue', but a question: I just realized that I do not understand a set of entries; why does one pull the embeddings into separate objects? Example:
umap_1 <- cystLineage2021_10[["umap"]]@cell.embeddings[,1]
(and two more lines for _2, and _3). These objects are not actually used for the plot, unless I am missing something obvious.

Great work, thanks for sharing!

Some Typos

1. plotting.data should be plot.data at line ~40

# Prepare a dataframe for cell plotting
plotting.data <- FetchData(object = yourseuratobject, vars = c("UMAP_1", "UMAP_2", "UMAP_3", "seurat_clusters"))



# Make a column of row name identities (these will be your cell/barcode names)
plot.data$label <- paste(rownames(plot.data))

2. pancreas.integrated should be yourseuratobject

3. Couple of suggestions

# create a dataframe
goi <- "TOP2A"
plotting.data <- FetchData(object = yourseuratobject, vars = c("UMAP_1", "UMAP_2", "UMAP_3", "Expression"=goi), slot = 'data')

# Say you want change the scale, so that every cell having an expression >1 will be one color
# Basically, you are re-adjusting the scale here, so that any cell having a certain expression will light up on your 3D plot

# First make another column in your dataframe, where all values above 1 are re-assigned a value of 1
# This information is stored in the 'Expression' column of your dataframe
# Cutoff <- 2
Cutoff <- quantile(plotting.data[,goi], probs = .95)
plotting.data$"ExprCutoff" <- ifelse(test = plotting.data[,goi] <Cutoff, yes = plotting.data[,goi], no = Cutoff)

# Add the label column, so that now the column has 'cellname-its expression value'
plotting.data$label <- paste(rownames(plotting.data)," - ", plotting.data[,goi], sep="")

# Plot your data, in this example my Seurat object had 21 clusters (0-20), and cells express a gene called ACTB
plot_ly(data = plotting.data,
        # name = goi,
        x = ~UMAP_1, y = ~UMAP_2, z = ~UMAP_3, 
        color = ~ExprCutoff, # you can just run this against the column for the gene as well using ~ACTB, the algorith will automatically scale in that case based on maximal and minimal values
        opacity = .5,
        colors = c('darkgrey', 'red'), 
        type = "scatter3d", 
        mode = "markers",
        marker = list(size = 1), 
        text=~label,
        hoverinfo="text"
) %>%layout(title=goi)

Hi,

not a problem as such, but I'd like to make this interactive 3D plot into a 3D animation where the plot spins on an axis continually. Is there a way I can do this?

Thanks in advance!

Alex

Hi!

Thanks for this nice script! It works like a charm ;)

I would like to make these plots more comparable to my 2D seurat plots. When you plot gene-expression values and re-scale for expression >1 that is similar to FeaturePlot is seurat, I guess.
Could you tell me how to apply the min.cutoff, max.cutoff arguments in the plot_ly plot?

Thanks!