Colour cells in t-SNE space by percentile gene expression

Source: R/feature_plots.R

Plot a low-dimensional embedding of the cells, coloured by expression percentile of a gene, of the total expression of a group of marker genes.

tsneByPercentileMarkerExpression(seurat, genes, reduction = "tsne",
  label = TRUE, palette = "blues", title = NULL, alpha = TRUE,
  legend = TRUE, legend_options = "percentiles", point_size = 1,
  label_repel = TRUE, label_size = 4, extra = FALSE,
  verbose = FALSE, hide_ticks = FALSE, label_short = FALSE,
  dim1 = 1, dim2 = 2)

Arguments

seurat

Seurat object, where dimensionality reduction has been applied, i.e. (after applying Seurat::RunPCA() or Seurat::RunTSNE() to the object)
genes

String or character vector specifying gene(s) to use
label

Logical, whether to label clusters on the plot. Default: TRUE.
palette

String or character vector. If a string, one of "viridis", "blues", or "redgrey", specifying which gradient palette to use. Otherwise, a character vector of colours (from low to high) to interpolate to create the scael. Default: "blues".
title

(Optional) string used as title for the plot.
alpha

Logical, whether to vary the alpha (point opacity) with percentile group to highlight cells in the top percentiles. If FALSE, sets a fixed opacity of 0.8. Default: TRUE.
legend

Logical, whether to plot the legend. Default: FALSE.
legend_options

String, "percentiles" or "values". Default: "percentiles".
point_size

Numeric, size of points in scatterplot. Default: 1. (A smaller value around 0.5 is better for plots which will be viewed at small scale.)
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.
extra

Logical, plot a detailed three-panel plot, where the first is a proportional bar plot of cells in each cluster in each percentile group, the second is a ridge plot showing density in each cluster of the mean expression of the markers (coloured by median percentile group within the cluster), and the third is the labelled tSNE plot coloured by percentiles. Requires label = TRUE. Default: FALSE. Default: FALSE.
verbose

Logical, whether to print status updates. Default: FALSE.
hide_ticks

Logical, whether to hide axis ticks. Default: FALSE
label_short

(Optional/Experimental!!) Logical, if TRUE, assumes clusters (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.

Value

A ggplot object

Examples

tsneByPercentileMarkerExpression(pbmc, "IL32")
dashboard(pbmc, "IL32", title = "Test dashboard")
#> Warning: Column `Cell` joining character vector and factor, coercing into character vector
#> Picking joint bandwidth of 1.08
feature(pbmc, "IL32")