plotProjections: Colour cells by a feature in two 2-dimension representation...
In ycl6/scRUtils: Single-Cell Sequencing Analysis Utilities

plotProjections

R Documentation

Colour cells by a feature in two 2-dimension representation side-by-side

Description

This function make use of plotProjection() to show cells on two pre-calculated low-dimensional projection (such as UMAP and t-SNE) in a compound figure.

Usage

plotProjections(
  sce,
  feature,
  dimnames = c("TSNE", "UMAP"),
  feat_desc = NULL,
  feat_color = NULL,
  color_breaks = waiver(),
  color_limits = NULL,
  exprs_by = "logcounts",
  text_by = NULL,
  point_size = 1,
  point_alpha = 0.5,
  theme_size = 18,
  show_na = FALSE,
  na.value = "grey50",
  legend_pos = "right",
  legend_just = "center",
  guides_ncol = NULL,
  guides_nrow = NULL,
  guides_barwidth = NULL,
  guides_barheight = NULL,
  guides_size = point_size * 2,
  titles = NULL,
  show_title = TRUE,
  show_subtitle = TRUE,
  other_fields = list(),
  add_void = FALSE,
  rel_widths = c(15, 1),
  rel_heights = c(15, 1),
  ...
)

Arguments

`sce`	A `SingleCellExperiment` object.
`feature`	A string indicating the column name in `colData(sce)` containing the feature to be coloured. Alternatively, a character vector of the same length as `colData(sce)` indicating the feature type of each cell.
`dimnames`	A character or integer vector of length 2 indicating the reduced dimension result in `reducedDims(sce)` to plot. Default is `c("TSNE", "UMAP")`.
`feat_desc`	A string that describes the coloured feature. Default is `NULL`.
`feat_color`	A character vector of colour codes indicating the colours of the features, or a palette function that creates a vector of colours along a colour map. Default is `NULL`, and use `choosePalette()` to select a palette.
`color_breaks`	For colouring continuous data, one of: `NULL` for no breaks `waiver()` for the default breaks (the scale limits) A character vector of breaks A function that takes the limits as input and returns breaks as output
`color_limits`	For colouring continuous data, one of: `NULL` to use the default scale range A numeric vector of length two providing limits of the scale. Use `NA` to refer to the existing minimum or maximum A function that accepts the existing (automatic) limits and returns new limits.
`exprs_by`	A string or integer scalar specifying which assay from `sce` to obtain expression values from, for use in point aesthetics. Use `assayNames(sce)` to find all availavle assays in `sce`. Default is "logcounts".
`text_by`	A string indicating the column metadata field with which to add text labels on the plot. Default is `NULL`.
`point_size`	A numeric scalar indicating the size of the points. Default is 1.
`point_alpha`	A numeric scalar (between 0 and 1) indicating the transparency. Default is 0.5.
`theme_size`	A numeric scalar indicating the base font size. Default is 18.
`show_na`	Logical scalar indicating whether to show `NA` values. Default is `FALSE`.
`na.value`	Colour to use for missing values. Default is `"grey50"`.
`legend_pos`	The position of legends ("none", "left", "right", "bottom","top". Use "none" to disable plot legend. Default is "right".
`legend_just`	The anchor point for positioning legend inside plot ("center" or two-element numeric vector) or the justification according to the plot area when positioned outside the plot. Default is "center".
`guides_ncol`, `guides_nrow`	An integer scalar indicating the desired number of column and row of discrete legends. Default is NULL.
`guides_barwidth`, `guides_barheight`	A numeric or a `grid::unit()` object specifying the width and height of the colourbar. Default is NULL.
`guides_size`	An integer scalar indicating the desired size of the points in a discrete legend. Default is `point_size * 2`.
`titles`	A character vector of length 2 indicating the plot title. Default is `NULL` and the `dimnames` is used as titles.
`show_title`	Logical scalar indicating whether to show plot title. Default is `TRUE`.
`show_subtitle`	Logical scalar indicating whether to show plot subtitle, Default is `TRUE`.
`other_fields`	Additional cell-based fields to include in the DataFrame. Default is `list()`.
`add_void`	Logical scalar indicating whether to add a completely empty theme using `ggplot2::theme_void()` in place of the legend. This is applicable when `legend_pos = "none"`. The empty theme is added to the right of the main plot using `plot_grid` Default is `FALSE`.
`rel_widths`	A numeric vector of relative columns widths. For example, in a two-column grid, `rel_widths = c(2, 1)` would make the first column twice as wide as the second column. This is applicable when `legend_pos` is "right" or "left". Default is `c(15, 1)` to make the joined plot 15 times as wide as the legend column if `legend_pos = "right"`.
`rel_heights`	A numerical vector of relative rows heights. Works just as `rel_widths` does, but for rows rather than columns. This is applicable when `legend_pos` is "bottom" or "top". Default is `c(15, 1)` to make the joined plot 15 times as tall as the legend row if `legend_pos = "bottom"`.
`...`	Other arguments passed on to `add_label()`.

Details

The function uses plotProjection() to create 2 base plots, then get_Legend() to produce a shared legend and plot_grid() from cowplot to create a compound figure with legend placed at the desired position as specified by legend_pos.

Value

A ggplot2 plot with an object of class c("gg", "ggplot")

Author(s)

I-Hsuan Lin

Examples

# Load demo dataset
data(sce)

# Plot TSNE and UMAP side-by-side
plotProjections(sce, "label",
  dimname = c("TSNE", "UMAP"), text_by = "label",
  feat_desc = "Cluster"
)

# Show DKD62 expression
plotProjections(sce, "DKD62",
  dimname = c("TSNE", "UMAP"), text_by = "label",
  feat_desc = "DKD62 Expression", guides_barwidth = 15
)

ycl6/scRUtils documentation built on Feb. 18, 2025, 6:14 a.m.