Plot dimensional reduction

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

plotPca(
  object,
  color_by = NULL,
  n_pcs = NULL,
  method_gs = NULL,
  pt_size = NULL,
  pt_alpha = NULL,
  pt_clrp = NULL,
  pt_clrsp = NULL,
  pt_clr = NULL,
  normalize = NULL,
  verbose = NULL,
  ...
)

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_size = NULL,
  pt_alpha = NULL,
  pt_clrsp = NULL,
  pt_clrp = NULL,
  pt_clr = NULL,
  clrp_adjust = NULL,
  normalize = NULL,
  use_scattermore = FALSE,
  sctm_interpolate = FALSE,
  sctm_pixels = c(1024, 1024),
  verbose = NULL,
  ...
)

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_size = NULL,
  pt_alpha = NULL,
  pt_clrsp = NULL,
  pt_clrp = NULL,
  pt_clr = NULL,
  clrp_adjust = NULL,
  normalize = NULL,
  transform_with = list(),
  use_scattermore = FALSE,
  sctm_interpolate = FALSE,
  sctm_pixels = c(1024, 1024),
  verbose = NULL,
  ...
)

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

Arguments

object

An object of class spata2.

color_by

The variable to be displayed by color:

• Gene set as a single character value. Must be in getGeneSets()

• Genes as a character vector. If more than one gene is specified the average expression of those genes will be calculated and displayed. Must be in getGenes()

• Feature as a single character value. Must be in getFeaturenNames()

n_pcs

Numeric value. Determines the number of principal components to be plotted. Must be an even number.

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().

pt_size

Numeric value. Specifies the size of all points.

pt_alpha

Numeric value. Specifies the degree of transparency 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.

pt_clr

Character value. Specifies the color of all points.

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.

verbose

Logical. If set to 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.

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.

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.

nrow, ncol

Numeric values or NULL. Used to arrange multiple plots.

transform_with

List or NULL. If list, can be used to transform continuous variables before plotting. Names of the list slots refer to the variable. The content of the slot refers to the transforming functions. Slot content can either be a character vector of function names. Use validScaleTransformations() to obtain all valid character value inputs. Or it can be a list of functions (and function names).

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.

Value

Returns a ggplot-object that can be additionally customized according to the rules of the ggplot2-framework.

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().