plot_spanning_tree {monocle} | R Documentation |
This function arranges all of the cells in the cds in a tree and predicts their location based on their pseudotime value
plot_spanning_tree(cds, x = 1, y = 2, color_by = "State", show_tree = TRUE, show_backbone = TRUE, backbone_color = "black", markers = NULL, show_cell_names = FALSE, cell_size = 1.5, cell_link_size = 0.75, cell_name_size = 2, show_branch_points = TRUE)
cds |
CellDataSet for the experiment |
x |
the column of reducedDimS(cds) to plot on the horizontal axis |
y |
the column of reducedDimS(cds) to plot on the vertical axis |
color_by |
the cell attribute (e.g. the column of pData(cds)) to map to each cell's color |
show_tree |
whether to show the links between cells connected in the minimum spanning tree |
show_backbone |
whether to show the diameter path of the MST used to order the cells |
backbone_color |
the color used to render the backbone. |
markers |
a gene name or gene id to use for setting the size of each cell in the plot |
show_cell_names |
draw the name of each cell in the plot |
cell_size |
The size of the point for each cell |
cell_link_size |
The size of the line segments connecting cells (when used with ICA) or the principal graph (when used with DDRTree) |
cell_name_size |
the size of cell name labels |
show_branch_points |
Whether to show icons for each branch point (only available when reduceDimension was called with DDRTree) |
a ggplot2 plot object
plot_cell_trajectory
## Not run: library(HSMMSingleCell) HSMM <- load_HSMM() plot_cell_trajectory(HSMM) plot_cell_trajectory(HSMM, color_by="Pseudotime", show_backbone=FALSE) plot_cell_trajectory(HSMM, markers="MYH3") ## End(Not run)