Function to plot gene expression — plot

Generate Hex Plot of a SpatialExperiment containing deconvolution results

Usage

plot_gene(
  spe,
  gene = NULL,
  assay = "counts",
  palette = "Mako",
  transform_scale = NULL,
  sample_id = "sample01",
  image_id = "lowres",
  reverse_palette = FALSE,
  show_image = FALSE,
  background = NULL,
  zoom = TRUE,
  palette_type = NULL,
  offset_rotation = FALSE,
  spot_size = 1,
  limits = NULL,
  smooth = FALSE,
  smoothing_factor = 1.5,
  show_legend = TRUE,
  title_size = 30,
  title = NULL,
  font_size = 15,
  legend_size = 20,
  density = TRUE,
  save = FALSE,
  path = NULL,
  png_width = 1500,
  png_height = 750,
  ...
)

Arguments

spe: deconvolution result in Form of a SpatialExperiment
gene: gene to plot
assay: assay to extract gene expression, default = "counts"
palette: colorspace palette (sequential)
transform_scale: data transform_scaleation to use, "log"
sample_id: sample id to plot, default: "sample01"
image_id: which image to plot, default: "lowres"
reverse_palette: reverse color palette
show_image: logical, whether to display the image, default = TRUE
background: custom background color
zoom: zoom to the available spots
palette_type: discrete, sequential or diverging
offset_rotation: correct hex orientation for rotated visium image
spot_size: increase (>1) or decrease (<1) the hex size
limits: vector of color scale limits
smooth: whether to smooth the plot
smoothing_factor: kernel size factor (multiples of spot distance)
show_legend: whether to show the legend
title_size: font size of title
title: set a custom title
font_size: font size of legend
legend_size: legend size in points
density: whether to display a density distribution next to the spatial plot
save: set TRUE to save plot
path: specify directory to save plot, if NULL: saving at ~/spacedeconv
png_width: when saving, png width in px
png_height: when saving, png height in px
...: additional paramters passed to internal functions

Value

plot of cell type fractions

Examples

data("spatial_data_2")
deconv <- spacedeconv::deconvolute(spatial_data_2, method = "estimate")
#> ── spacedeconv ─────────────────────────────────────────────────────────────────
#> ℹ testing parameter
#> ✔ parameter OK [16ms]
#> 
#> 
#> 
#> ── Spatial 
#> Assays: "counts"
#> Genes: 36591
#> → without expression: 13411 (36.65%)
#> Spots: 1310
#> Spots under tissue: 1310 (100%)
#> Median Genes Per Spot: 4613.5
#> → without expression: 15 (1.15%)
#> Umi count range: 0 - 64683
#> Spots with UMI count below 500: 85 (0.23%)
#> ✔ Rownames set
#> ✔ Colnames set
#> ℹ deconvoluting
#> Error in loadNamespace(x): there is no package called ‘immunedeconv’
#> ✖ deconvoluting [249ms]
#> 
spacedeconv::plot_celltype(deconv, cell_type = "estimate_immune.score")
#> Error in eval(expr, envir, enclos): object 'deconv' not found