spatInSituPlotPoints#
Last Updated: Oct 02, 2023
Description#
Function to plot multiple features for multiple modalities at the spatial in situ level
Usage#
spatInSituPlotPoints(
gobject,
show_image = F,
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",
point_size = 1.5,
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 = c("blue", "white", "red"),
polygon_fill_gradient_midpoint = NULL,
polygon_fill_as_factor = NULL,
polygon_fill_code = NULL,
polygon_alpha = 0.5,
polygon_line_size = 2,
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"),
show_plot = NA,
return_plot = NA,
save_plot = NA,
save_param = list(),
default_save_name = "spatInSituPlotPoints",
verbose = TRUE
)
Arguments#
|
giotto object |
|
show a tissue background image |
|
a giotto image |
|
name of a giotto image |
|
name of a giottoLargeImage |
|
spatial unit |
|
name of spatial locations |
|
features to plot |
|
feature types of the feats |
|
code to color the provided features |
|
code to shape the provided feature types |
|
spatial dimension x |
|
spatial dimension y |
|
size of the points |
|
expand feature coordinate counts (see details) |
|
column name with count information (if expand_counts = TRUE) |
|
maximum x,y jitter provided as c(x, y) |
|
overlay polygon information (e.g. cell shape) |
|
use polygon and feature coordinates overlap results |
|
feature type associated with polygon information |
|
color for polygon border |
|
color for polygon background (overruled by polygon_fill) |
|
fill color or column for polygon |
|
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 |
|
is fill color a factor |
|
code to color the fill column |
|
alpha of polygon |
|
line width of the polygon’s outline |
|
axis text size |
|
title text size |
|
legend text size |
|
fix ratio of coordinates |
|
background color |
|
show legend |
|
method to plot points |
|
show plots |
|
return ggplot object |
|
directly save the plot [boolean] |
|
list of saving parameters, see
|
|
default save name for saving, don’t change, change save_name in save_param |
|
verbosity |
Details#
TODO
Value#
ggplot
See Also#
Other In Situ visualizations: spatInSituPlotDensity()
,
spatInSituPlotHex()