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spatInSituPlotDensity

Source: R/vis_spatial_in_situ.R
spatInSituPlotDensity.Rd

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,
  polygon_size = deprecated(),
  polygon_line_size = 0.5,
  coord_fix_ratio = 1,
  axis_text = 8,
  axis_title = 8,
  legend_text = 6,
  background_color = "black",
  cow_n_col = NULL,
  cow_rel_h = 1,
  cow_rel_w = 1,
  cow_align = "h",
  show_plot = NULL,
  return_plot = NULL,
  save_plot = NULL,
  save_param = list(),
  default_save_name = "spatInSituPlotDensity"
)

Arguments

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 (e.g. cell shape)

polygon_feat_type

feature type associated with polygon information

polygon_color

color for polygon border. Set NA to remove border

polygon_fill

character. what to color to fill polgyons by (e.g. metadata col or spatial enrichment col)

polygon_fill_as_factor

is fill color a factor

polygon_alpha

alpha of polygon

polygon_size

deprecated

polygon_line_size

line width of the polygon's outline

coord_fix_ratio

fix ratio between x and y-axis

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 heights of rows (e.g. c(1,2))

cow_rel_w

cowplot param: relative widths of columns (e.g. c(1,2))

cow_align

cowplot param: how to align

show_plot

logical. show plot

return_plot

logical. return ggplot object

save_plot

logical. save the plot

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

ggplot

Details

TODO

See also

Other In Situ visualizations: spatInSituPlotHex(), spatInSituPlotPoints()

Examples

g <- GiottoData::loadGiottoMini("vizgen")
#> 1. read Giotto object
#> 2. read Giotto feature information
#> 3. read Giotto spatial information
#> 3.1 read Giotto spatial shape information
#> 3.2 read Giotto spatial centroid information
#> 3.3 read Giotto spatial overlap information
#> 4. read Giotto image information
#> python already initialized in this session
#>  active environment : '/usr/bin/python3'
#>  python version : 3.10
#> checking default envname 'giotto_env'
#> a system default python environment was found
#> Using python path:
#>  "/usr/bin/python3"
spatInSituPlotDensity(g, feats = c("Mlc1", "Gprc5b", "Gfap"),
polygon_feat_type = "z0")