spatInSituPlotPoints

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

Usage

spatInSituPlotPoints(
  gobject,
  show_image = FALSE,
  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",
  spat_enr_names = NULL,
  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 = NULL,
  polygon_fill_gradient_midpoint = NULL,
  polygon_fill_gradient_style = c("divergent", "sequential"),
  polygon_fill_as_factor = NULL,
  polygon_fill_code = NULL,
  polygon_alpha = NULL,
  polygon_line_size = 0.4,
  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"),
  plot_last = c("polygons", "points"),
  theme_param = list(),
  show_plot = NULL,
  return_plot = NULL,
  save_plot = NULL,
  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 or multiple images with group_by
largeImage_name: deprecated
spat_unit: spatial unit (e.g. "cell")
spat_loc_name: name of spatial locations
feats: named list of 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
spat_enr_names: character. names of spatial enrichment results to include
point_size: size of the points
stroke: stroke to apply to feature points
expand_counts: expand feature coordinate counts (see details)
count_info_column: column name with count information (if expand_counts = TRUE)
jitter: numeric. Maximum x,y jitter provided as c(x, y) or a single number which will be recycled to length 2.
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. Set NA to remove border
polygon_bg_color: color for polygon background (overruled by polygon_fill)
polygon_fill: character. what to color to fill polgyons by (e.g. metadata col or spatial enrichment col)
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_gradient_style: either 'divergent' (midpoint is used in color scaling) or 'sequential' (scaled based on data range)
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
plot_last: which layer to show on top of plot, polygons (default) or points.
theme_param: list of additional params passed to ggplot2::theme()
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
verbose: be verbose

Value

ggplot

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

# plot the number detected features in the `giotto` object.
spatInSituPlotPoints(
    g,
    polygon_feat_type = "aggregate",
    polygon_fill = "nr_feats",
    polygon_fill_as_factor = FALSE,
    polygon_fill_gradient_style = "sequential",
    polygon_line_size = 0.1,
    polygon_alpha = 1
)
#> plot polygon layer done


# plot the same as above, but with the first 4 rna features plotted as
# detection points. Also add in the background and change the polygon
# alpha and border color
spatInSituPlotPoints(
    g,
    polygon_feat_type = "aggregate",
    polygon_fill = "nr_feats",
    polygon_fill_as_factor = FALSE,
    polygon_fill_gradient_style = "sequential",
    polygon_line_size = 0.1,
    polygon_alpha = 0.4,
    polygon_color = "magenta",
    feats = list("rna" = GiottoClass::featIDs(g)[1:4]),
    point_size = 0.8,
    plot_last = "points",
    show_image = TRUE,
    image_name = "dapi_z0"
)
#> plot image layer done
#> plot polygon layer done
#> --| Plotting 1360 feature points
#> plot feature points layer done


# plot with spatial enrichment information
spatInSituPlotPoints(
    g,
    polygon_feat_type = "aggregate",
    spat_enr_names = "cluster_metagene",
    polygon_fill = "1",
    polygon_fill_as_factor = FALSE,
    polygon_fill_gradient_style = "sequential",
    polygon_alpha = 1
)
#> plot polygon layer done

Usage

Arguments

Value

See also

Examples