plotSurface: Plot the surface of the sample
In theMILOlab/SPATA2: A Toolbox for Spatial Expression Analysis

plotSurface

R Documentation

Plot the surface of the sample

Description

Displays the spatial dimension of the sample and colors the surface according to the expression of genes, gene sets or features. There are methods for multiple classes:

SPATA2: The most versatile method with which all sorts of spatial data can be visualized.
data.frame: Method for a data.frame that contains at least the variables x and y.
SpatialAnnotationScreening: Method to visualize the surface based on the setup with which spatialAnnotationScreening() was run.
SpatialTrajectoryScreening: Method to visualize the surface based on the setup with which spatialAnnotationScreening() was run.

Usage

plotSurface(object, ...)

## S4 method for signature 'SPATA2'
plotSurface(
  object,
  color_by = NULL,
  alpha_by = NULL,
  smooth = FALSE,
  smooth_span = 0.2,
  pt_alpha = NULL,
  pt_clr = NULL,
  pt_clrp = NULL,
  pt_clrsp = NULL,
  pt_size = NULL,
  outline = FALSE,
  outline_fct = c(2.125, 2.75),
  clrp_adjust = NULL,
  transform_with = NULL,
  use_scattermore = NULL,
  sctm_pixels = c(1024, 1024),
  bcs_rm = base::character(0),
  na_rm = FALSE,
  xrange = getCoordsRange(object)$x,
  yrange = getCoordsRange(object)$y,
  display_image = NULL,
  img_alpha = 1,
  img_name = NULL,
  geom = "point",
  mtr_name = activeMatrix(object),
  verbose = NULL,
  ...
)

## S4 method for signature 'data.frame'
plotSurface(
  object,
  color_by = NULL,
  alpha_by = NULL,
  pt_alpha = 0.9,
  pt_clr = "lightgrey",
  pt_clrp = "milo",
  pt_clrsp = "inferno",
  pt_size = 2,
  image = NULL,
  clrp_adjust = NULL,
  use_scattermore = FALSE,
  sctm_pixels = c(1024, 1024),
  sctm_interpolate = FALSE,
  outline = FALSE,
  outline_coords = NULL,
  outline_fct = c(2.125, 2.75),
  order_by = NULL,
  order_desc = FALSE,
  na_rm = TRUE,
  ...
)

## S4 method for signature 'SpatialAnnotationScreening'
plotSurface(
  object,
  color_by = "rel_loc",
  line_color = "black",
  line_size = 1,
  fill = ggplot2::alpha("lightgrey", 0.25),
  pt_clrp = "npg",
  ...
)

## S4 method for signature 'SpatialGradientScreening'
plotSurface(
  object,
  color_by = "rel_loc",
  line_color = "black",
  line_size = 1,
  pt_clrp = "npg",
  ...
)

plotSurfaceInteractive(object)

Arguments

`object`	An object of class `SPATA2` or, in case of S4 generics, objects of classes for which a method has been defined.
`...`	Additional arguments given to `scale_color_add_on()`.
`color_by`	Character value. The variables by which to color the data points.
`smooth`	Logical. If TRUE, a loess fit is used to smooth the values.
`smooth_span`	Numeric value. Controls the degree of smoothing. Given to argument `span` of `stats::loess()`.
`pt_alpha`	Numeric value. Specifies the degree of transparency of all points.
`pt_clr`	Character value. Specifies the color 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_size`	Numeric value. Specifies the size of all points.
`outline`	Logical, indicating whether to add an outline to the points. If `TRUE`, an outline will be added around the points to enhance visibility. Default is FALSE.
`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.
`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.
`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.
`bcs_rm`	Character vector or `NULL`. If character, specifies the observations to be removed prior to analysis or visualization by their barcode.
`xrange`, `yrange`	Distance vector of length two or `NULL`. If not `NULL`, specifies the x- and y-range to which the spatial output is cropped. E.g. `xrange = c(200, 500)` results in the two dimensional space being cropped from x-coordinate 200px up to x-coordinate 500px. If `NULL`, the original range is used.
`img_alpha`	Numeric value. Sets the transparency for the image.
`img_name`	Character value. The name of the image of interest. If `NULL`, the active image is chosen by default. Either way, must be one of `getImageNames()`.
`mtr_name`	Character value. The name of the matrix of interest. Defaults to the active matrix of the assay, as denoted by `activateMatrix()`.
`verbose`	Logical. If `TRUE`, informative messages regarding the computational progress will be printed. (Warning messages will always be printed.)
`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`.
`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`.
`line_color`	Character. Affects color of the main lines of the plot.
`line_size`	Numeric. Affects size of the main lines of the plot.
`fill`	Character value or NA. If character, specifies the color with which the outline of the spatial annotation is filled.
`outline_width`	Numeric vector of length 2, specifying the factor with which the `pt_size` is multiplied to create the white layer (first value) and the black layer (second value).

Value

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

Note

The methods for SpatialAnnotationScreening- and SpatialTrajectoryScreening exist to quickly visualize the set up with which the screening was conducted. The ... can be used to reach the plotSurface() method for data.frames with all its plotting parameters. For more controll, please use a combination of plotSurface() with the SPATA2 object and ⁠ggpLayer*⁠ functions.