Plot the sample

Displays the spatial dimension of the sample and colors the surface according to the expression of genes, gene sets or features.

  • plotSurface() Takes the spata-object as the starting point and creates the necessary data.frame from scratch according to additional parameters.

  • plotSurface2() Takes a data.frame as the starting point.

  • plotSurfaceInteractive() Takes only the spata-object and opens a shiny application which allows for interactive plotting.

plotSurface(
  object,
  of_sample = "",
  color_to = NULL,
  method_gs = "mean",
  normalize = TRUE,
  smooth = FALSE,
  smooth_span = 0.02,
  pt_size = 2,
  pt_alpha = 1,
  pt_clrsp = "inferno",
  pt_clrp = "milo",
  pt_clr = "lightgrey",
  display_image = FALSE,
  display_title = FALSE,
  assign = FALSE,
  assign_name,
  verbose = TRUE
)

plotSurface2(
  coords_df,
  color_to,
  pt_size = 2,
  pt_alpha = 0.9,
  pt_clrsp = "inferno",
  pt_clrp = "milo",
  image = NULL
)

plotSurfaceInteractive(object)

Arguments

object

A valid spata-object.
of_sample

The sample(s) of interest specified as a single character value or vector. If set to "" (the default) the first sample is chosen.
color_to

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().
smooth

Logical. If set to TRUE values will be smoothed according to the smoooth_-parameters.
smooth_span

The amount of smoothing specified as a single numeric value.
pt_size

The size of the points specified as a single numeric value.
pt_alpha

The transparency of the points specified as single numeric value.
pt_clrsp

The color spectrum to be used if the specified variable displayed by color is continuous. Run all_colorspectra() to see valid input..
pt_clrp

The color panel to be used if the specified variable displayed by color is categorical/discrete. Run all_colorpanels() to see valid input.
pt_clr

The base color of every point displayed in the plot.
display_image

Logical. If set to TRUE the histology image of the specified sample is displayed underneath the plot.
display_title

Logical. If set to TRUE an informative title is displayed.
assign

Logical. If set to TRUE a named list will be assigned to the global environment. This list contains data and information to rebuild or additionally customize the output plot of this function.
assign_name

The name the assigned list is supposed to have specified as a single character value.
verbose

Logical. If set to TRUE informative messages regarding the computational progress will be printed.

(Warning messages will always be printed.)
coords_df

A data.frame containing information about every barcode-spot. Must contain the variables:

barcodes

Character. The barcode-sequences (+ the sample belonging) of every barcode spot.

sample

Character. The sample belonging of every barcode-spot.

x

Numeric. The x-coordinates of every barcode.

y

Numeric. The y-coordinates of every barcode.
image

An image of class Image to be displayed in the background. Easily accessible via SPATA::image().