Different Ways to Visualize Spatial Data¶
This section delves into the multiple different ways that Giotto provides to visualize your spatial data.
Check out the different dataset examples to see the wide range of visualization options.
1. Task/Analysis Specific Functions¶
2. Functions that use the Spatial Coordinates of a Cell/Spot¶
These functions generally start with spatXXX
3. Functions that use the Dimension Reduction Coordinates of a Cell/Spot¶
These functions generally start with dimXXX
4. Functions for co-visualization that combine spat (2) and dim (3)¶
5. Both in 2D and 3D¶
Most functions both have a 2D and 3D version, like spatDimPlot2D() and spatDimPlot3D(). In those cases the spatDimPlot2D() is the same as spatDimPlot(). So only in case you want to plot your spatial or dimension reduction data in 3D, you need to specifically say so.
6. Ways to Save Plots¶
Giotto Tips and Tricks: How to visualize and save plots in Giotto? for more information.
All parameters available to save_param() are found on the help page of ?Giotto::all_plots_save_function
7. Hypothetical Example¶
# 1. standard R way pl = spatPlot(mygobject, cell_color = 'cell_types') pdf(file = 'path/to/save/to/plot.pdf') print(pl) dev.off() # 2. indicate to save plot, this will save the plot according to Giotto instructions file # If the instruction file is not provided in the beginning, it uses the defaults (e.g. working directory) spatPlot(mygobject, cell_color = 'cell_types', save_plot = TRUE) # 3. indicate to save plot and specifiy specific saving parameters by providing a list to save_param # they will overrule the giotto instructions spatPlot(mygobject, cell_color = 'cell_types', save_plot = TRUE, save_param = list(save_folder = 'my_subfolder', save_name = 'my_name', save_format = 'png', units = 'in')) # 4. don't save or return plot, but just view plot # defaults are: save_plot = F, return_plot = T and show_plot = T # this can be changed in the instructions file or at each specific plotting function spatPlot(mygobject, cell_color = 'cell_types', save_plot = F, return_plot = F show_plot = T)