group name error

[CMSimpson8]

I am having an issue using SCORPIUS, I want to set my progression group to show my Seurat clusters and the trajectory line between them - I am getting this error

Error in check_numeric_vector(progression_group, "progression_group", :
‘progression_group’ must be a numeric vector consisting of 2833 finite number(s)

the guide suggests setting the group name to Seuratobject$sample_info$group_name
I have group set to mySeuratobject$meta.data$seurat_clusters

Is this the wrong subfile to set my group to? Which is the correct?
I'm using R3.6.

Thanks!

[CMSimpson8]

Issue was partially solved by using
as.numeric(data@seurat_clusters$[,1]) and
contour = FALSE in the progression graph

[VivianQM]

Running into the same error...

[asif7adil]

Hi!
The progression_group expects a factor value. You have to change the numeric or character valued column/group of your metadata as factor. Like following:

Get the Group type from the metadata as a vector

group = c(metadata$group_col)

change the group to factor

group <- as.factor(group)

hope this helps.

[shaln]

I have tried the above suggestions but still getting the error. My group names are 'Control_D5', 'Control_D7', 'Control_D9'. I have also tried swapping the group names to the cluster numbers instead (0-8) but still had the error.

> control
An object of class Seurat 
58153 features across 16728 samples within 2 assays 
Active assay: SCT (24615 features, 2000 variable features)
 3 layers present: counts, data, scale.data
 1 other assay present: RNA
 2 dimensional reductions calculated: pca, umap

> space <- reduce_dimensionality(control@assays$SCT@data, dist = "spearman", ndim = 3)
> control_group <- as.factor(control@meta.data$orig.ident)
> draw_trajectory_plot(space, progression_group = control_group, contour = TRUE)
Error in check_numeric_vector(progression_group, "progression_group",  : 
  ‘progression_group’ must be a numeric vector consisting of 24615 finite number(s)

Any help re this would be much appreciated!

[asif7adil]

before converting your control group to a factor, it has to be taken as a vector.
try this:

control_group <- c(control@meta.data$orig.ident)

control_group <- as.factor(control_group)

draw_trajectory_plot(space, progression_group = control_group, contour = TRUE)

Hope this helps!

[shaln]

Hi @asif7adil, thanks for the suggestion! I'm afraid the same error still persists after trying that :(

> control_group <- c(control@meta.data$orig.ident)
> control_group <- as.factor(control_group)
> draw_trajectory_plot(space, progression_group = control_group, contour = TRUE)
Error in check_numeric_vector(progression_group, "progression_group",  : 
  ‘progression_group’ must be a numeric vector consisting of 24615 finite number(s)

> class(control_group)
[1] "factor"
> class(control_group[1])
[1] "factor"

[liufymed]

Hi, I met the same issue with you guys:
draw_trajectory_plot(P_space, group_name, contour = TRUE)
Error in check_numeric_vector(progression_group, "progression_group", :
‘progression_group’ must be a numeric vector consisting of 17941 finite `number(s).

I thought there might be something wrong with the expression matrix so I used t() and had primarily solved it:

expression <-t(P_seurat@assays$RNA@layers$counts)
group_name<- P_seurat$HPC_clusters
group_name <-as.factor(group_name)
P_space <- reduce_dimensionality(expression, "spearman")
draw_trajectory_plot(P_space, group_name, contour = TRUE)

Hope it can help you.
Sincerely,
Fangyi