spatInSituPlotDensity#

Date

2022-10-06

https://github.com/drieslab/Giotto/tree/suite/R/spatial_in_situ_visuals.R#L909

Description#

Function for density plots for features for multiple modalities at the spatial in situ level

Usage#

spatInSituPlotDensity(
  gobject,
  feats = NULL,
  feat_type = "rna",
  sdimx = "x",
  sdimy = "y",
  alpha = 0.95,
  show_polygon = TRUE,
  polygon_feat_type = "cell",
  polygon_color = "black",
  polygon_fill = NULL,
  polygon_fill_as_factor = NULL,
  polygon_alpha = 0.5,
  axis_text = 8,
  axis_title = 8,
  legend_text = 6,
  background_color = "black",
  cow_n_col = 2,
  cow_rel_h = 1,
  cow_rel_w = 1,
  cow_align = "h",
  show_plot = NA,
  return_plot = NA,
  save_plot = NA,
  save_param = list(),
  default_save_name = "spatInSituPlotDensity"
)

Arguments#

Argument

Description

gobject

giotto object

feats

features to plot

feat_type

feature types of the feats

sdimx

spatial dimension x

sdimy

spatial dimension y

alpha

alpha of density plot

show_polygon

overlay polygon information (cell shape)

polygon_feat_type

feature type associated with polygon information

polygon_color

color for polygon border

polygon_fill

fill color or column for polygon

polygon_fill_as_factor

is fill color a factor

polygon_alpha

alpha of polygon

axis_text

axis text size

axis_title

title text size

legend_text

legend text size

background_color

background color

cow_n_col

cowplot param: how many columns

cow_rel_h

cowplot param: relative height

cow_rel_w

cowplot param: relative width

cow_align

cowplot param: how to align

show_plot

show plots

return_plot

return ggplot 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

Details#

TODO

Value#

ggplot

Seealso#

Other In Situ visualizations: `spatInSituPlotHex <#spatinsituplothex>`__ , `spatInSituPlotPoints <#spatinsituplotpoints>`__