showPattern3D#

Date

2022-10-06

https://github.com/drieslab/Giotto/tree/suite/R/spatial_genes.R#L2644

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#

Argument

Description

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 `showSaveP arameters <#showsaveparameters>`__

default_save_name

default save name for saving, don’t change, change save_name in save_param

Value#

plotly