spatInSituPlotPoints | R Documentation |
Function to plot multiple features for multiple modalities at the spatial in situ level
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,
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 = 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
)
gobject |
giotto object |
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_unit |
spatial unit |
spat_loc_name |
name of spatial locations |
feats |
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 |
point_size |
size of the points |
expand_counts |
expand feature coordinate counts (see details) |
count_info_column |
column name with count information (if expand_counts = TRUE) |
jitter |
maximum x,y jitter provided as c(x, y) |
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 |
polygon_bg_color |
color for polygon background (overruled by polygon_fill) |
polygon_fill |
fill color or column for polygon |
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 |
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 |
show_plot |
show plots |
return_plot |
return ggplot object |
save_plot |
directly save the plot [boolean] |
save_param |
list of saving parameters, see |
default_save_name |
default save name for saving, don't change, change save_name in save_param |
verbose |
verbosity |
line |
line size of point shapes |
TODO
ggplot
Other In Situ visualizations:
spatInSituPlotDensity()
,
spatInSituPlotHex()
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