spatInSituPlotHex#

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Last Updated: Mar 11, 2023

Description#

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

Usage#

spatInSituPlotHex(
  gobject,
  feats = NULL,
  feat_type = "rna",
  sdimx = "x",
  sdimy = "y",
  binwidth = NULL,
  min_axis_bins = 10,
  alpha = 0.5,
  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 = "white",
  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 = "spatInSituPlotHex"
)

Arguments#

`gobject`	giotto object
`feats`	features to plot
`feat_type`	feature types of the feats
`sdimx`	spatial dimension x
`sdimy`	spatial dimension y
`binwidth`	numeric vector for x and y width of bins (default is minor axis range/10, where the 10 is from `min_axis_bins`)
`min_axis_bins`	number of bins to create per range defined by minor axis. (default value is 10)
`alpha`	alpha of hexbin 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: spatInSituPlotDensity(), spatInSituPlotPoints()