highlight: Highlight select clusters on a dimensionality reduction plot

In fungenomics/cytobox: A toolbox for analyzing single cell RNA-seq data

Description

Plot the embedding for the dataset, with cells from select clusters coloured by either their original colours or provided colours, and cells from all other clusters in another (non-intrusive) colour, or not at all. This is a thin wrapper for tsne which takes care of specifying cells and colours in order to highlight the desired clusters.

Usage

highlight(seurat, clusters = NULL, cells = NULL, reduction = "tsne",
  original_colours = NULL, default_colour = "gray90",
  label_all = FALSE, label = TRUE, ...)

Arguments

seurat	Seurat object, where Seurat::RunTSNE() has been applied
clusters	Vector of one or more clusters to highlight, matching the levels at levels(seurat@ident). If "none", all clusters are coloured by default_colour.
cells	Character vector of cell IDs specifying cells to highlight.
original_colours	(Optional) Vector of colours to use. Either one colour per cluster, in the order of levels(seurat@ident), or one colour per cluster passed to clusters, in the other they were provided. Default: default ggplot2 colours used by Seurat.
default_colour	String, colour to use for non-highlighted clusters, or "none", if cells in those clusters should not be plot at all. Default: gray80 (light grey).
label_all	Logical, if labelling the tSNE (if label == TRUE), whether to label all the clusters, or only the ones being highlighted. Default: FALSE.
...	Arguments passed on to plot_dr 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 [e-mail] by which to colour cells. Default: NULL, colour cells by cluster (in seurat@ident). 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. 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. title (Optional) String specifying title. 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 hide_axes Logical, whether to hide axis labels. Default: TRUE 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. highlight_cells Character vector of cell names if only a subset of cells should be coloured in the plot (these should correspond to [e-mail]). 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 [e-mail], 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 [e-mail], 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. 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 dim1 Numeric, dimension of embedding to use for x-axis. Default = 1. dim2 Numeric, dimension of embedding to use for y-axis. Default = 2.

Value

A ggplot2 object

Author(s)

Selin Jessa

Examples

# Highlight cluster 3 on the tSNE plot
highlight(pbmc, 3)

# Pass additional arguments to cytobox::tsne
highlight(pbmc, c(2, 3), label = FALSE, title = "Test highlight")

# Change default colour
highlight(pbmc, c(2, 3), default_colour = "lightblue")

# Specify the colours to highlight the clusters with
highlight(pbmc, c(2, 3), c("red", "blue"))

# Don't plot cells in other clusters
highlight(pbmc, c(2, 3), default_colour = "none")

fungenomics/cytobox documentation built on Feb. 13, 2020, 10:51 a.m.