highlight: Highlight select clusters on a tSNE plot
In sjessa/cytokit: A toolkit for analyzing single cell RNA-seq data

Description Usage Arguments Value Author(s) Examples

Plot the tSNE 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.

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

`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`.
`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 `plotDR` 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`). 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. point_size Numeric, size of points in scatter plot. Default: 0.6 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. Default: FALSE 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. cells Character vector of cell names if only a subset of cells should be 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. 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. na_color 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.

A ggplot2 object

Selin Jessa

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

# Pass additional arguments to cytokit::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")