View source: R/GEX_trajectories.R
GEX_trajectories | R Documentation |
This is a function which infers trajectories along ordered cells on dimensionality reduced data. It projects trajectrories on a dim. red. plot such as Umap. This uses Monocle3 or Monocle2.
GEX_trajectories( GEX, color.cells.by, reduction.method, cluster.method, genes, label.cell.groups, label.groups.by.cluster, labels.per.group, group.label.size, monocle.version, ordering.cells.method )
GEX |
GEX output of the VDJ_GEX_matrix function (VDJ_GEX_matrix[[2]])) |
color.cells.by |
Column name in SummarizedExperiment::colData(GEX). To decide how the cells are colored in the output plot. E.g. color.cells.by = 'group_id' the cells will be colored based on their group_id. |
reduction.method |
Which method to use for dimensionality reduction for monocle3. Supports "UMAP", "tSNE", "PCA" or "LSI". Default value is "UMAP". |
cluster.method |
Monocle3 gives two clustering options: Using the Leiden or the Louvain algo. Default is louvain. |
genes |
Takes a vector of genes (e.g. genes = c('CD3E', 'CD4', 'CD8A', 'CD44')) to highlight the expression of these genes in UMAP and in the trajectory plot in monocle3. Default is NULL. |
label.cell.groups |
Whether to label cells in each group according to the most frequently occurring label(s) (as specified by color_cells_by) in the group. If false, plot_cells() simply adds a traditional color legend. Default is TRUE |
label.groups.by.cluster |
Instead of labeling each cluster of cells, place each label once, at the centroid of all cells carrying that label. Default is TRUE |
labels.per.group |
How many labels to plot for each group of cells. Default is 1 |
group.label.size |
Font size to be used for cell group labels. Default is 1 |
monocle.version |
Version of monocle. Either monocle2 or monocle3. Default is monocle3. |
ordering.cells.method |
In monocle2 you can choose between selecting genes with high dispersion across cells for ordering cells along a trajectory (= 'high.dispersion'). Or order cells based on genes which differ between clusters, uses an unsupervised procedure called "dpFeature" (= 'differ.genes'). Defalut is "differ.genes" |
Returns a list.For monocle3: Element [[1]] returns a cell data set object with a new column for the UMAP clustering. This will be used for the GEX_pseudotime_trajectory_plot() function. [[2]] contains a plot of the clusters. [[3]] contains also a cluster plot but with the inferred trajectories. For monocle2: [[1]] cell data set object. [[2]] Trajetory plot with cells coloured based on their states (important to choose root state for pseudotime plot). [[3]] Trajectory plot based on color.cells.by
## Not run: trajectory_output <- GEX_trajectories(GEX = vgm[[2]], reduction.method = "UMAP", color.cells.by = "group_id", labels_per_group = 2, group_label_size = 3) #visualizing gene expressions interesting_genes = c("Cxcr6", "Il7r") genes_trajectories <- GEX_trajectories(GEX = VGM$GEX, color.cells.by = "group_id", genes = interesting_genes) ##monocle2 ! DEPRECATED ! #trajectory_output <- GEX_trajectories(GEX = vgm[[2]], # monocle.version = "monocle2", # ordering.cells.method = "high.dispersion") ## End(Not run)
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