spatInSituPlotDensity: spatInSituPlotDensity

In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

spatInSituPlotDensity

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,
  polygon_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 = NA,
  return_plot = NA,
  save_plot = NA,
  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 (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
polygon_size	size of polygon border
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 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 showSaveParameters
default_save_name	default save name for saving, don't change, change save_name in save_param

Details

TODO

Value

ggplot

See Also

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

drieslab/Giotto_site_suite documentation built on April 26, 2023, 11:51 p.m.