plotSurface: Plot the surface of the sample
In kueckelj/SPATA2: A Toolbox for Spatial Gene 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.

plotSurface() Takes the SPATA2 object or a data.frame.
plotSurfaceInteractive() Takes only the SPATA2 object and opens a shiny application which allows for interactive plotting.

Usage

plotSurface(object, ...)

## S4 method for signature 'spata2'
plotSurface(
  object,
  color_by = NULL,
  alpha_by = NULL,
  method_gs = NULL,
  normalize = NULL,
  smooth = FALSE,
  smooth_span = NULL,
  pt_alpha = NULL,
  pt_clr = NULL,
  pt_clrp = NULL,
  pt_clrsp = NULL,
  pt_size = NULL,
  pt_size_fixed = NULL,
  clrp_adjust = NULL,
  use_scattermore = FALSE,
  sctm_pixels = c(1024, 1024),
  sctm_interpolate = FALSE,
  display_image = NULL,
  display_title = NULL,
  complete = NULL,
  verbose = NULL,
  highlight_groups = NULL,
  transform_with = NULL,
  bcsp_rm = NULL,
  na_rm = FALSE,
  pt_size_legend = 10,
  order_by = NULL,
  order_desc = FALSE,
  ...
)

## 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,
  order_by = NULL,
  order_desc = FALSE,
  na_rm = TRUE,
  ...
)

plotSurfaceInteractive(object)

Arguments

`object`	An object of class `spata2`.
`...`	Used to absorb deprecated arguments or functions.
`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()`
`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().
`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.
`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.
`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`.
`display_image`	Logical. If set to TRUE the histology image of the specified sample is displayed underneath the plot.
`display_title`	Logical value. If set to TRUE an informative title is displayed.
`complete`	Logical. If the provided `SPATA2` object has been subsetted by `subsetBySegment()` the original sample is completed with grey barcode spots.
`verbose`	Logical. If set to TRUE informative messages regarding the computational progress will be printed. (Warning messages will always be printed.)
`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.
`bcsp_rm`	Character vector or `NULL.` If character, specifies barcode-spots that are removed before analysis or plotting.
`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`.
`image`	An image of class Image to be displayed in the background. Easily accessible via `SPATA::image()`.