In this vignette, SCORPIUS is used to infer a trajectory through cells in artificial single-cell RNA-seq data. Note that the dataset is generated in a very naive manner and is only meant to be used for demonstration purposes, not for evaluating trajectory inference methods.
Expression values for 384 cells and 500 genes is generated as follows.
library(SCORPIUS) <- generate_dataset(num_genes = 500, num_samples = 384, num_groups = 4)dataset
The resulting dataset is a list containing a matrix named
expression and a data frame named
expression is a 384-by-500 matrix containing the expression values of all the cells and all the genes.
## Gene1 Gene2 Gene3 Gene4 Gene5 Gene6 ## Sample1 4.229293 0.000000 6.752726 2.911327 9.116873 7.968772 ## Sample2 12.063623 6.101313 0.000000 8.023840 6.612786 0.000000 ## Sample3 7.973086 12.969934 10.412038 5.564873 10.258806 0.000000 ## Sample4 0.000000 10.665796 7.329762 4.635637 9.743435 5.462945 ## Sample5 8.467850 12.182375 5.609669 0.000000 7.102293 7.985970 ## Sample6 9.269898 9.630904 10.455783 0.000000 8.349845 13.157807
sample_info is a data frame with the metadata of the cells, containing only the group each cell belongs to.
## group_name ## Sample1 Group 1 ## Sample2 Group 1 ## Sample3 Group 1 ## Sample4 Group 1 ## Sample5 Group 1 ## Sample6 Group 1
In order to infer a trajectory through this data, SCORPIUS first reduces the dimensionality of the dataset.
SCORPIUS uses Torgerson multi-dimensional scaling to reduce the dataset to three dimensions. This technique attempts to place the cells in a space such that the distance between any two points in that space approximates the original distance between the two cells as well as possible.
The distance between any two samples is defined as their correlation distance, namely
1 - (cor(x, y)+1)/2. The reduced space is constructed as follows:
<- dataset$expression expression <- dataset$sample_info$group_name group_name <- reduce_dimensionality(expression, "spearman", ndim = 3)space
The new space is a 384-by-3 matrix, and can be visualised with or without colouring of the different cell types.
draw_trajectory_plot(space, progression_group = group_name, contour = TRUE)
The main goal of SCORPIUS is to infer a trajectory through the cells, and orden the cells according to the inferred timeline.
SCORPIUS infers a trajectory through several intermediate steps, which are all executed as follows:
The result is a list containing the final trajectory
path and the inferred timeline for each sample
The trajectory can be visualised with respect to the samples by passing it to
draw_trajectory_plot( space, progression_group = group_name, path = traj$path, contour = TRUE )
We search for genes whose expression is seems to be a function of the trajectory timeline that was inferred, as such genes might be good candidate marker genes for the dynamic process that is being investigated.
<- gene_importances(expression, traj$time, num_permutations = 0, num_threads = 8) gimp <- gimp[1:50,] gene_sel <- expression[,gene_sel$gene]expr_sel
To visualise the expression of the selected genes, use the
draw_trajectory_heatmap(expr_sel, traj$time, group_name)
Finally, these genes can also be grouped into modules as follows:
<- extract_modules(scale_quantile(expr_sel), traj$time, verbose = FALSE) modules draw_trajectory_heatmap(expr_sel, traj$time, group_name, modules)