spatInSituPlotPoints: spatInSituPlotPoints

In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

spatInSituPlotPoints

Description

Function to plot multiple features for multiple modalities at the spatial in situ level

Usage

spatInSituPlotPoints(
  gobject,
  show_image = F,
  gimage = NULL,
  image_name = NULL,
  largeImage_name = NULL,
  spat_unit = NULL,
  spat_loc_name = NULL,
  feats = NULL,
  feat_type = "rna",
  feats_color_code = NULL,
  feat_shape_code = NULL,
  sdimx = "x",
  sdimy = "y",
  point_size = 1.5,
  stroke = 0.5,
  expand_counts = FALSE,
  count_info_column = "count",
  jitter = c(0, 0),
  show_polygon = TRUE,
  use_overlap = TRUE,
  polygon_feat_type = "cell",
  polygon_color = "black",
  polygon_bg_color = "black",
  polygon_fill = NULL,
  polygon_fill_gradient = c("blue", "white", "red"),
  polygon_fill_gradient_midpoint = NULL,
  polygon_fill_as_factor = NULL,
  polygon_fill_code = NULL,
  polygon_alpha = 0.5,
  polygon_line_size = 2,
  axis_text = 8,
  axis_title = 8,
  legend_text = 6,
  coord_fix_ratio = 1,
  background_color = "black",
  show_legend = TRUE,
  plot_method = c("ggplot", "scattermore", "scattermost"),
  show_plot = NA,
  return_plot = NA,
  save_plot = NA,
  save_param = list(),
  default_save_name = "spatInSituPlotPoints",
  verbose = TRUE
)

Arguments

gobject	giotto object
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_unit	spatial unit
spat_loc_name	name of spatial locations
feats	features to plot
feat_type	feature types of the feats
feats_color_code	code to color the provided features
feat_shape_code	code to shape the provided feature types
sdimx	spatial dimension x
sdimy	spatial dimension y
point_size	size of the points
expand_counts	expand feature coordinate counts (see details)
count_info_column	column name with count information (if expand_counts = TRUE)
jitter	maximum x,y jitter provided as c(x, y)
show_polygon	overlay polygon information (e.g. cell shape)
use_overlap	use polygon and feature coordinates overlap results
polygon_feat_type	feature type associated with polygon information
polygon_color	color for polygon border
polygon_bg_color	color for polygon background (overruled by polygon_fill)
polygon_fill	fill color or column for polygon
polygon_fill_gradient	polygon fill gradient colors given in order from low to high
polygon_fill_gradient_midpoint	value to set as gradient midpoint (optional). If left as NULL, the median value detected will be chosen
polygon_fill_as_factor	is fill color a factor
polygon_fill_code	code to color the fill column
polygon_alpha	alpha of polygon
polygon_line_size	line width of the polygon's outline
axis_text	axis text size
axis_title	title text size
legend_text	legend text size
coord_fix_ratio	fix ratio of coordinates
background_color	background color
show_legend	show legend
plot_method	method to plot points
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
verbose	verbosity
line	line size of point shapes

Details

TODO

Value

ggplot

See Also

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

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