spatInSituPlotPoints#

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Last Updated: Mar 11, 2023

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,
  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

Details#

TODO

Value#

ggplot

See Also#

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