Function to plot deconvolution results
plot_most_abundant.RdGenerate Hex Plot of a SpatialExperiment containing the most abundant cell types
Usage
plot_most_abundant(
spe,
method = NULL,
cell_type = NULL,
remove = NULL,
min_spot = 0,
palette = "Mako",
sample_id = "sample01",
image_id = "lowres",
reverse_palette = FALSE,
show_image = FALSE,
background = NULL,
zoom = TRUE,
palette_type = "discrete",
offset_rotation = FALSE,
spot_size = 1,
title_size = 30,
font_size = 15,
legend_size = 20,
density = FALSE,
save = FALSE,
path = NULL,
png_width = 1500,
png_height = 750,
title = NULL,
show_legend = TRUE,
min_abundance = 0.01,
...
)Arguments
- spe
deconvolution result in Form of a SpatialExperiment
- method
select which results should be displayed
- cell_type
one or more celltype to plot, NULL for all
- remove
vector of cell types to be removed from the plot
- min_spot
minimum number of spots the cell-type has to be present in
- palette
colorspace palette (sequential)
- 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
logical, whether to scale the color palette_type, default = FALSE
- offset_rotation
correct hex orientation for rotated visium image
- spot_size
increase (>1) or decrease (<1) the hex size
- title_size
font size of 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
- title
set a custom title
- show_legend
whether to show the legend
- min_abundance
minimum abundance of celltypes to be included in the analysis
- ...
additional paramters passed to internal functions