plotUmap: Plot dimensional reduction

In theMILOlab/SPATA2: A Toolbox for Spatial Expression Analysis

Plot dimensional reduction

Description

Displays the dimensional reduction and maps gene, gene-set or feature information onto the color-aesthetic.

Usage

plotPCA(
  object,
  color_by = NULL,
  n_pcs = NULL,
  pt_alpha = 0.9,
  pt_clr = "lightgrey",
  pt_size = 1,
  pt_clrp = NULL,
  pt_clrsp = NULL,
  nrow = NULL,
  ncol = NULL,
  verbose = NULL,
  ...
)

plotPca(...)

plotTSNE(
  object,
  color_by = NULL,
  color_aes = "color",
  color_trans = "identity",
  alpha_by = NULL,
  order_by = NULL,
  order_desc = FALSE,
  pt_shape = 19,
  shape_by = NULL,
  method_gs = NULL,
  pt_alpha = 0.9,
  pt_clr = "lightgrey",
  pt_size = 1,
  pt_clrsp = NULL,
  pt_clrp = NULL,
  clrp_adjust = NULL,
  normalize = NULL,
  use_scattermore = FALSE,
  sctm_interpolate = FALSE,
  sctm_pixels = c(1024, 1024),
  verbose = NULL,
  ...
)

plotTsne(...)

plotTsneComparison(
  object,
  color_by,
  ggpLayers = list(),
  display_title = FALSE,
  nrow = NULL,
  ncol = NULL,
  ...
)

plotUMAP(
  object,
  color_by = NULL,
  color_aes = "color",
  color_trans = "identity",
  alpha_by = NULL,
  order_by = NULL,
  order_desc = FALSE,
  shape_by = NULL,
  method_gs = NULL,
  pt_shape = 19,
  pt_alpha = 0.9,
  pt_clr = "lightgrey",
  pt_size = 1,
  pt_clrsp = NULL,
  pt_clrp = NULL,
  clrp_adjust = NULL,
  normalize = NULL,
  transform_with = list(),
  use_scattermore = FALSE,
  sctm_interpolate = FALSE,
  sctm_pixels = c(1024, 1024),
  verbose = NULL,
  ...
)

plotUmap(...)

plotUmapComparison(
  object,
  color_by,
  ggpLayers = list(),
  display_title = FALSE,
  nrow = NULL,
  ncol = NULL,
  ...
)

Arguments

object	An object of class SPATA2 or, in case of S4 generics, objects of classes for which a method has been defined.
color_by	Character value. The variables by which to color the data points.
n_pcs	Numeric value. Determines the number of principal components to be plotted. Must be an even number.
pt_alpha	Numeric value. Specifies the degree of transparency of all points.
pt_clr	Character value. Specifies the color of all points.
pt_size	Numeric value. Specifies the size of all points.
pt_clrp	The color palette to be used if the specified variable displayed by color is categorical/discrete. Run validColorPalettes() to see valid input.
pt_clrsp	The color spectrum to be used if the specified variable displayed by color is continuous. Run validColorSpectra() to see valid input.
nrow, ncol	Numeric values or NULL. Used to arrange multiple plots.
verbose	Logical. If TRUE, informative messages regarding the computational progress will be printed. (Warning messages will always be printed.)
...	Used to absorb deprecated arguments or functions.
order_by	Character value or NULL. If character, the specified variable is used to order the data points.
order_desc	Logical value. If TRUE, reverses the arrangement specified via order_by and/or order.
method_gs	Character value. The method according to which gene sets will be handled specified as a character of length one. This can be either 'mean or one of 'gsva', 'ssgsea', 'zscore', or 'plage'. The latter four will be given to gsva::GSVA().
clrp_adjust	Named character vector or NULL. If character, it adjusts the color palette that is used to represent the groups. Names of the input vector must refer to the group and the respective named element denotes the color with which to represent the group.
normalize	Logical. If set to TRUE values will be scaled to 0-1. Hint: Variables that are uniformly expressed can not be scaled and are discarded.
use_scattermore	Logical value. If TRUE, data points are plotted with scattermore::geom_scattermore() which allows quick plotting of several thousand data points. If the number of data points plotted is bigger than 10.000 it is used anyway.
sctm_interpolate, sctm_pixels	Given to the corresponding arguments of scattermore::geom_scattermore(). Note: With increasing sctm_pixels the point size must be adjusted with the argument pt_size.
ggpLayers	A list of ggplot add ons to add to each plot.
display_title	Logical value. If set to TRUE an informative title is displayed.
transform_with	List or NULL. If list, can be used to transform continuous variables before usage. Names of the list slots refer to the variable. The content of the slot refers to the transforming functions. E.g if the variable of interest is GFAP gene expression, the following would work: Single function: transform_with = log10, Multiple functions: ⁠transform_with = list(GFAP = list(log10, log2)⁠ In case of plotting: Useful if you want to apply more than one transformation on variables mapped to plotting aesthetics. Input for transform_with is applied before the respective <aes>_trans argument.

Details

The comparison version of each function take a vector of variables to color by. A list of plots is created that is arranged via grid.arrange().

Value

A ggplot.

Examples

library(SPATA2)

data("example_data")

object <- example_data$object_UKF269T_diet

object <- runPCA(object)
object <- runTSNE(object)
object <- runUMAP(object)

plotPCA(object, color_by = "histology")
plotTSNE(object, color_by = "histology")
plotUMAP(object, color_by = "histology")

theMILOlab/SPATA2 documentation built on Feb. 8, 2025, 11:41 p.m.