spatDeconvPlot#

Date

2022-10-06

https://github.com/drieslab/Giotto/tree/suite/R/spatial_visuals.R#L3538

Description#

Visualize cell type enrichment / deconvolution results in a scatterpie

Usage#

spatDeconvPlot(
  gobject,
  spat_unit = NULL,
  feat_type = NULL,
  deconv_name = "DWLS",
  show_image = F,
  gimage = NULL,
  image_name = NULL,
  largeImage_name = NULL,
  spat_loc_name = NULL,
  sdimx = "sdimx",
  sdimy = "sdimy",
  cell_color_code = NULL,
  line_color = NA,
  radius = 10,
  alpha = 1,
  legend_text = 8,
  background_color = "white",
  title = NULL,
  axis_text = 8,
  axis_title = 8,
  coord_fix_ratio = TRUE,
  show_plot = NA,
  return_plot = NA,
  save_plot = NA,
  save_param = list(),
  default_save_name = "spatDeconvPlot"
)

Arguments#

Argument

Description

gobject

giotto object

spat_unit

spatial unit

feat_type

feature type

deconv_name

name of deconvolution results to use

show_image

show a tissue background image

gimage

a giotto image

image_name

name of a giotto image

largeImage_name

name of a giottoLargeImage

spat_loc_name

name of spatial locations

sdimx

x-axis dimension name (default = ‘sdimx’)

sdimy

y-axis dimension name (default = ‘sdimy’)

cell_color_code

named vector with colors

line_color

color of line within pie charts

radius

radios of pie charts

alpha

alpha of pie charts

legend_text

size of legend text

background_color

color of plot background

title

title for plot (default = deconv_name)

axis_text

size of axis text

axis_title

size of axis title

coord_fix_ratio

fix ratio between x and y-axis

show_plot

show plot

return_plot

return ggplot object

save_plot

directly save the plot [boolean]

save_param

list of saving parameters from `all_plots_save_f unction <#allplotssavefunction>`__

default_save_name

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

Details#

Description of parameters.

Value#

ggplot