showPattern3D: showPattern3D

In bernard2012/Giotto: Spatial single-cell transcriptomics toolbox

Description

show patterns for 3D spatial data

Usage

showPattern3D(
  gobject,
  spatPatObj,
  dimension = 1,
  trim = c(0.02, 0.98),
  background_color = "white",
  grid_border_color = "grey",
  show_legend = T,
  point_size = 1,
  axis_scale = c("cube", "real", "custom"),
  custom_ratio = NULL,
  x_ticks = NULL,
  y_ticks = NULL,
  z_ticks = NULL,
  show_plot = NA,
  return_plot = NA,
  save_plot = NA,
  save_param = list(),
  default_save_name = "showPattern3D"
)

Arguments

gobject	giotto object
spatPatObj	Output from detectSpatialPatterns
dimension	dimension to plot
trim	Trim ends of the PC values.
background_color	background color for plot
grid_border_color	color for grid
show_legend	show legend of plot
point_size	adjust the point size
axis_scale	scale the axis
custom_ratio	cutomize the scale of the axis
x_ticks	the tick number of x_axis
y_ticks	the tick number of y_axis
z_ticks	the tick number of z_axis
show_plot	show plot
return_plot	return plot object
save_plot	directly save the plot [boolean]
save_param	list of saving parameters, see showSaveParameters
default_save_name	default save name for saving, don't change, change save_name in save_param

Value

plotly

Examples

    showPattern3D(gobject)

bernard2012/Giotto documentation built on Sept. 22, 2020, 10:29 a.m.