plotFourStates: Gene set state plot

In kueckelj/SPATA: A Toolbox for Spatial Gene Expression Analysis

Gene set state plot

Description

Takes four gene sets and visualizes the relative expression of these four gene sets for every barcode by computing it's respective x- and y- coordinates in the state plot. (See details.)

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

• plotFourStates2() Takes a data.frame as input.

Usage

plotFourStates(
  object,
  of_sample = "",
  states,
  color_to = NULL,
  method_gs = "mean",
  average_genes = FALSE,
  pt_size = 1.5,
  pt_alpha = 0.9,
  pt_clrsp = "inferno",
  pt_clrp = "milo",
  display_labels = TRUE,
  assign = FALSE,
  assign_name,
  verbose = TRUE
)

plotFourStates2(
  data,
  states,
  color_to = NULL,
  pt_size = 1.5,
  pt_alpha = 0.9,
  pt_clrsp = "inferno",
  pt_clrp = "milo",
  display_labels = TRUE
)

Arguments

states	The gene sets defining the four states specified as a character vector of length 4.
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()
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.
verbose	Logical. If set to TRUE informative messages regarding the computational progress will be printed. (Warning messages will always be printed.)
data	A data.frame containing at least the variables barcodes, states.. Whereby the states-variables contain the respective expression values of the specified gene sets.

Value

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

kueckelj/SPATA documentation built on March 22, 2022, 9:59 p.m.