plot_dr: Plot a reduced dimensionality embedding for a Seurat object,...
In fungenomics/cytobox: A toolbox for analyzing single cell RNA-seq data

Description Usage Arguments Value Functions Author(s) Examples

Plot a reduced dimensionality embedding for a Seurat object, colouring by cluster or arbitrary variables.

plot_dr(seurat, reduction = "tsne", colour_by = NULL, colours = NULL,
  colour_by_type = "discrete", label = TRUE,
  point_size = ifelse(length(seurat@cell.names) > 300, 0.6, 1.3),
  alpha = 0.8, legend = ifelse((is.null(colour_by)) && (label), FALSE,
  TRUE), label_repel = TRUE, label_size = 4, highlight_cells = NULL,
  show_all_cells = TRUE, order_by = NULL, clusters_to_label = NULL,
  hide_ticks = TRUE, title = NULL, label_short = FALSE,
  na_colour = "gray80", limits = NULL, constrain_scale = TRUE,
  hide_axes = FALSE, dim1 = 1, dim2 = 2, border_colour = NULL,
  border_size = NULL)

tsne(seurat, ...)

pca(seurat, ...)

umap(seurat, ...)

phate(seurat, ...)

`seurat`	Seurat object, where Seurat::RunTSNE() has been applied
`reduction`	String, specifying a lot of `seurat@dr`, which indicates which embedding to plot. Default: "tsne". (Can also take "umap" or "pca").
`colour_by`	(Optional) String, specifying the column in `seurat@meta.data` by which to colour cells. Default: NULL, colour cells by cluster (in `seurat@ident`).
`colours`	(Optional) Character vector of colours for points. If `colour_by` is NULL, cells will be coloured by cluster; this should be a named character vector of colours for points. Names should correspond to cluster names (e.g. `levels(seurat@ident)`). If specifying `colour_by`, and the variable is discrete, this should be a character vector, with either names or order corresponding to categorical values in the column of `seurat@meta.data` specified. Otherwise, if the variable is continuous, pass the gradient to use, or a few colours (from low to high) from which a gradient should be created, and specify `colour_by_type = "continuous"`. The default is to use ggplot2 colours.
`colour_by_type`	(Optional) String, one of "discrete" or "continuous". If specifying `colour_by` and providing colours to the `colours` argument, specify whether the `colour_by` variable is discrete or continuous. Default: discrete. The function is pretty good at setting the palette correctly on its own, but try modifying this in case of errors.
`label`	Logical, whether to plot cluster labels. Default: TRUE
`point_size`	Numeric, size of points in scatter plot. Default: 0.6 for datasets with < 300 cells, and 1.3 for datasets with otherwise.
`alpha`	Numeric, fixed alpha value for points: Default: 0.8
`legend`	Logical, whether to plot legend. Default: FALSE if `colour_by` is NULL and `label` is TRUE, true otherwise.
`label_repel`	Logical, if `label` is TRUE, whether to plot cluster labels repelled from the center, on a slightly transparent white background and with an arrow pointing to the cluster center. If FALSE, simply plot the cluster label at the cluster center. Default: TRUE.
`label_size`	Numeric, controls the size of text labels. Default: 4.
`highlight_cells`	Character vector of cell names if only a subset of cells should be coloured in the plot (these should correspond to seurat@cell.names). Default: Plot all cells. See the argument `clusters_to_label` for only labelling certain clusters. See the `constrain_scale` argument for controlling the scales of the plot.
`show_all_cells`	Logical. When passing cells to `highlight_cells`, if TRUE, plot the remaining cells in `na_colour`, if FALSE, only plot the highlighted cells. Default: TRUE.
`order_by`	String, corresponding to a column in `seurat@meta.data`, specifying a variable to control the order in which cells are plot. (Thus, you can manually specify the order, add it as a new column in `seurat@meta.data`, and pass that). If numeric, cells with high values are plot on top. If not, the column must be a factor, and cells will be ordered according to the levels, with cells in the first level plot on top. Default: if a numeric column is specified to `colour_by`, sort by that variable, otherwise, use the ordering of the cells in the Seurat object.
`clusters_to_label`	(Optional.) If `label` is TRUE, clusters for which labels should be plot (if only a subset of clusters should be labelled). Default: NULL (Label all clusters).
`hide_ticks`	Logical, whether to hide axis ticks, i.e. both the text and the small lines indicating the breaks along the x- and y-axes. Default: FALSE
`title`	(Optional) String specifying title.
`label_short`	(Optional/Experimental!!) Logical, if TRUE, assumes cluster names (at seurat@ident) consist of a prefix and a suffix separated by a non-alpha numeric character (`"[^[:alnum:]]+"`), and tries to separate these names and only plot the prefix, for shorter labels and a cleaner plot. Default: FALSE.
`na_colour`	String, specifying the colour (built-in or hex code) to use to plot points which have an NA value, for example in the variable specified in `colour_by`. Default: light gray ("gray80), change to "white" to purposely hide those cells. If you do not want to plot certain cells at all, pass names of cells to plot to the `cells` argument.
`limits`	Numeric vector of length two providing the lower and upper limits of the colour scale, if colouring by a continuous variable. Default: min and max of the values the variable takes on in the data.
`constrain_scale`	Logical, if plotting a subset of cells, whether to use the limits of the tSNE embedding computed on the whole dataset (useful for constraining scales across plots while only plotting specific cells). Default: TRUE
`hide_axes`	Logical, whether to hide axis labels. Default: TRUE
`dim1`	Numeric, dimension of embedding to use for x-axis. Default = 1.
`dim2`	Numeric, dimension of embedding to use for y-axis. Default = 2.

A ggplot2 object

tsne: Plot a tSNE embedding
pca: Plot a PCA embedding
umap: Plot a UMAP embedding
phate: Plot a PHATE embedding

Selin Jessa

tsne(pbmc)

# Demonstrate label_short:
# Set cluster IDs to be too long
pbmc2 <- pbmc
levels(pbmc2@ident) <- c("1-Cell type A", "2-Cell type B", "3-Cell type C", "4-Cell type D")
tsne(pbmc2)

# Plot the prefixes only
tsne(pbmc2, label_short = TRUE)

# Only colour cells in cluster 3
plot_dr(pbmc, highlight_cells = whichCells(pbmc, clusters = 3))

# Plot the # of genes for only cells in cluster 3, but display all cells on the plot
tsne(pbmc, highlight_cells = whichCells(pbmc, clusters = 3), colour_by = "nGene",
show_all_cells = FALSE, colours = viridis::viridis(100), colour_by_type = "continuous")