spatInSituPlotHex#
Last Updated: Jan 14, 2025
Description#
Function to plot hexbins for features for multiple modalities at the spatial in situ level
Usage#
spatInSituPlotHex(
gobject,
feats = NULL,
feat_type = "rna",
sdimx = "x",
sdimy = "y",
binwidth = NULL,
min_axis_bins = 10,
alpha = 0.5,
show_polygon = TRUE,
polygon_feat_type = "cell",
polygon_color = "black",
polygon_fill = NULL,
polygon_fill_as_factor = NULL,
polygon_alpha = 0.5,
polygon_size = 0.5,
coord_fix_ratio = 1,
axis_text = 8,
axis_title = 8,
legend_text = 6,
background_color = "white",
cow_n_col = NULL,
cow_rel_h = 1,
cow_rel_w = 1,
cow_align = "h",
show_plot = NA,
return_plot = NA,
save_plot = NA,
save_param = list(),
default_save_name = "spatInSituPlotHex"
)
Arguments#
|
giotto object |
|
features to plot |
|
feature types of the feats |
|
spatial dimension x |
|
spatial dimension y |
|
numeric vector for x and y width
of bins (default is minor axis
range/10, where the 10 is from
|
|
number of bins to create per range defined by minor axis. (default value is 10) |
|
alpha of hexbin plot |
|
overlay polygon information (cell shape) |
|
feature type associated with polygon information |
|
color for polygon border |
|
fill color or column for polygon |
|
is fill color a factor |
|
alpha of polygon |
|
size of polygon border |
|
fix ratio between x and y-axis |
|
axis text size |
|
title text size |
|
legend text size |
|
background color |
|
cowplot param: how many columns |
|
cowplot param: relative height |
|
cowplot param: relative width |
|
cowplot param: how to align |
|
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 |
Details#
TODO
Value#
ggplot
See Also#
Other In Situ visualizations: spatInSituPlotDensity()
,
spatInSituPlotPoints()