Visualize cell type enrichment / deconvolution results in a scatterpie
Usage
spatDeconvPlot(
gobject,
spat_unit = NULL,
feat_type = NULL,
deconv_name = "DWLS",
show_image = FALSE,
gimage = NULL,
image_name = NULL,
largeImage_name = NULL,
spat_loc_name = NULL,
sdimx = "sdimx",
sdimy = "sdimy",
cell_color_code = NULL,
line_color = NA,
radius = 10,
alpha = 1,
legend_text = 8,
background_color = "white",
title = NULL,
axis_text = 8,
axis_title = 8,
coord_fix_ratio = 1,
show_plot = NULL,
return_plot = NULL,
save_plot = NULL,
save_param = list(),
theme_param = list(),
default_save_name = "spatDeconvPlot"
)Arguments
- gobject
giotto object
- spat_unit
spatial unit (e.g. "cell")
- feat_type
feature type (e.g. "rna", "dna", "protein")
- deconv_name
name of deconvolution results to use
- show_image
show a tissue background image
- gimage
a giotto image
- image_name
name of a giotto image
- largeImage_name
name of a giottoLargeImage
- spat_loc_name
name of spatial locations
- sdimx
x-axis dimension name (default = 'sdimx')
- sdimy
y-axis dimension name (default = 'sdimy')
- cell_color_code
character. discrete colors to use. palette to use or named vector of colors
- line_color
color of line within pie charts
- radius
radios of pie charts
- alpha
alpha of pie charts
- legend_text
size of legend text
- background_color
color of plot background
- title
title for plot (default = deconv_name)
- axis_text
size of axis text
- axis_title
size of axis title
- coord_fix_ratio
fix ratio between x and y-axis
- 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- theme_param
list of additional params passed to
ggplot2::theme()- default_save_name
default save name for saving, don't change, change save_name in save_param