plot_cell_trajectory: Plots the minimum spanning tree on cells.

In monocle: Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq

Description

Plots the minimum spanning tree on cells.

Usage

plot_cell_trajectory(cds, x = 1, y = 2, color_by = "State",
  show_tree = TRUE, show_backbone = TRUE, backbone_color = "black",
  markers = NULL, use_color_gradient = FALSE, markers_linear = FALSE,
  show_cell_names = FALSE, show_state_number = FALSE, cell_size = 1.5,
  cell_link_size = 0.75, cell_name_size = 2, state_number_size = 2.9,
  show_branch_points = TRUE, theta = 0, ...)

Arguments

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
use_color_gradient	Whether or not to use color gradient instead of cell size to show marker expression level
markers_linear	a boolean used to indicate whether you want to scale the markers logarithimically or linearly
show_cell_names	draw the name of each cell in the plot
show_state_number	show state number
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
state_number_size	the size of the state number
show_branch_points	Whether to show icons for each branch point (only available when reduceDimension was called with DDRTree)
theta	How many degrees you want to rotate the trajectory
...	Additional arguments passed into scale_color_viridis function

Value

a ggplot2 plot object

Examples

## Not run: 
lung <- load_lung()
plot_cell_trajectory(lung)
plot_cell_trajectory(lung, color_by="Pseudotime", show_backbone=FALSE)
plot_cell_trajectory(lung, markers="MYH3")

## End(Not run)

Example output

Loading required package: Matrix
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:Matrix':

    colMeans, colSums, rowMeans, rowSums, which

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: ggplot2
Loading required package: VGAM
Loading required package: stats4
Loading required package: splines
Loading required package: DDRTree
Loading required package: irlba
Removing 4 outliers
There were 50 or more warnings (use warnings() to see the first 50)

monocle documentation built on Nov. 8, 2020, 5:06 p.m.