plotPlatePosition: Plot cells in plate positions

In Alanocallaghan/scater: Single-Cell Analysis Toolkit for Gene Expression Data in R

Plot cells in plate positions

Description

Plots cells in their position on a plate, coloured by metadata variables or feature expression values from a SingleCellExperiment object.

Usage

plotPlatePosition(
  object,
  plate_position = NULL,
  colour_by = color_by,
  size_by = NULL,
  shape_by = NULL,
  order_by = NULL,
  by_exprs_values = "logcounts",
  add_legend = TRUE,
  theme_size = 24,
  point_alpha = 0.6,
  point_size = 24,
  point_shape = 19,
  other_fields = list(),
  swap_rownames = NULL,
  color_by = NULL,
  by.assay.type = by_exprs_values
)

Arguments

object	A SingleCellExperiment object.
plate_position	A character vector specifying the plate position for each cell (e.g., A01, B12, and so on, where letter indicates row and number indicates column). If NULL, the function will attempt to extract this from object$plate_position. Alternatively, a list of two factors ("row" and "column") can be supplied, specifying the row (capital letters) and column (integer) for each cell in object.
colour_by	Specification of a column metadata field or a feature to colour by, see the by argument in ?retrieveCellInfo for possible values.
size_by	Specification of a column metadata field or a feature to size by, see the by argument in ?retrieveCellInfo for possible values.
shape_by	Specification of a column metadata field or a feature to shape by, see the by argument in ?retrieveCellInfo for possible values.
order_by	Specification of a column metadata field or a feature to order points by, see the by argument in ?retrieveCellInfo for possible values.
by_exprs_values	Alias for by.assay.type.
add_legend	Logical scalar specifying whether a legend should be shown.
theme_size	Numeric scalar, see ?"scater-plot-args" for details.
point_alpha	Numeric scalar specifying the transparency of the points, see ?"scater-plot-args" for details.
point_size	Numeric scalar specifying the size of the points, see ?"scater-plot-args" for details.
point_shape	An integer, or a string specifying the shape of the points. See ?"scater-plot-args" for details.
other_fields	Additional cell-based fields to include in the data.frame, see ?"scater-plot-args" for details.
swap_rownames	Column name of rowData(object) to be used to identify features instead of rownames(object) when labelling plot elements.
color_by	Alias to colour_by.
by.assay.type	A string or integer scalar specifying which assay to obtain expression values from, for use in point aesthetics - see the assay.type argument in ?retrieveCellInfo.

Details

This function expects plate positions to be given in a charcter format where a letter indicates the row on the plate and a numeric value indicates the column. Each cell has a plate position such as "A01", "B12", "K24" and so on. From these plate positions, the row is extracted as the letter, and the column as the numeric part. Alternatively, the row and column identities can be directly supplied by setting plate_position as a list of two factors.

Value

A ggplot object.

Author(s)

Davis McCarthy, with modifications by Aaron Lun

Examples

example_sce <- mockSCE()
example_sce <- logNormCounts(example_sce)

## define plate positions
example_sce$plate_position <- paste0(
    rep(LETTERS[1:5], each = 8), 
    rep(formatC(1:8, width = 2, flag = "0"), 5)
)

## plot plate positions
plotPlatePosition(example_sce, colour_by = "Mutation_Status")

plotPlatePosition(example_sce, shape_by = "Treatment", 
    colour_by = "Gene_0004")

plotPlatePosition(example_sce, shape_by = "Treatment", size_by = "Gene_0001",
    colour_by = "Cell_Cycle")

Alanocallaghan/scater documentation built on July 18, 2024, 10:58 p.m.