spatInSituPlotHex | R Documentation |
Function to plot hexbins for features for multiple modalities at the spatial in situ level
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"
)
gobject |
giotto object |
feats |
features to plot |
feat_type |
feature types of the feats |
sdimx |
spatial dimension x |
sdimy |
spatial dimension y |
binwidth |
numeric vector for x and y width of bins (default is minor axis
range/10, where the 10 is from |
min_axis_bins |
number of bins to create per range defined by minor axis. (default value is 10) |
alpha |
alpha of hexbin plot |
show_polygon |
overlay polygon information (cell shape) |
polygon_feat_type |
feature type associated with polygon information |
polygon_color |
color for polygon border |
polygon_fill |
fill color or column for polygon |
polygon_fill_as_factor |
is fill color a factor |
polygon_alpha |
alpha of polygon |
polygon_size |
size of polygon border |
coord_fix_ratio |
fix ratio between x and y-axis |
axis_text |
axis text size |
axis_title |
title text size |
legend_text |
legend text size |
background_color |
background color |
cow_n_col |
cowplot param: how many columns |
cow_rel_h |
cowplot param: relative height |
cow_rel_w |
cowplot param: relative width |
cow_align |
cowplot param: how to align |
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 |
TODO
ggplot
Other In Situ visualizations:
spatInSituPlotDensity()
,
spatInSituPlotPoints()
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