spatInSituPlotHex

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 = deprecated(),
  polygon_line_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 = NULL,
  return_plot = NULL,
  save_plot = NULL,
  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 (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

Examples

g <- GiottoData::loadGiottoMini("vizgen")
#> 1. read Giotto object
#> 2. read Giotto feature information
#> /home/runner/work/_temp/Library/GiottoData/Mini_datasets/Vizgen/VizgenObject/Features/rna_feature_spatVector.shp
#> rna
#> 3. read Giotto spatial information
#> 3.1 read Giotto spatial shape information
#> aggregate_spatInfo_spatVector.shp z0_spatInfo_spatVector.shp
#>  z1_spatInfo_spatVector.shp
#> aggregate
#> z0
#> z1
#> 
#> 3.2 read Giotto spatial centroid information
#> aggregate
#> z0
#> z1
#> 
#> 3.3 read Giotto spatial overlap information
#> rna_aggregate_spatInfo_spatVectorOverlaps.shp
#>  rna_z0_spatInfo_spatVectorOverlaps.shp rna_z1_spatInfo_spatVectorOverlaps.shp
#> poly_ID feat_ID feat_ID_uniq stack
#> aggregate and rna
#> poly_ID feat_ID feat_ID_uniq
#> z0 and rna
#> poly_ID feat_ID feat_ID_uniq
#> z1 and rna
#> 
#> 4. read Giotto image information
#> 
#> no external python path or giotto
#>  environment was specified, will check if a
#>  default python path is available
#> 
#> A default python path was found: /usr/bin/python3 and will be used
#>  If this is not the correct python path, either
#> 
#> 1. use installGiottoEnvironment() to install
#>  a local miniconda python environment along with required modules
#> 
#> 2. provide an existing python path to
#>  python_path to use your own python path which has all modules
#>  installed
#> Set options("giotto.use_conda" = FALSE) if
#>  python functionalities are not needed
spatInSituPlotHex(g, feats = c("Mlc1", "Gprc5b", "Gfap"),
polygon_feat_type = "z0")
#> Error: package 'hexbin' is not yet installed
#> 
#>  To install:
#> install.packages(c("hexbin"))

Usage

Arguments

Value

Details

See also

Examples