In RubD/Giotto_site: Spatial Single-Cell Transcriptomics Toolbox

Different ways to visualize your spatial data?

Giotto provides different ways to visualize your spatial data:

1. Functions specific to a task or analysis:

plotHeatmap
plotMetadataHeatmap
violinPlot
... check out the different dataset examples to see the wide range of visualization options

2. Functions that use the spatial coordinates of each cell or spot, they usually start with spatXXX

spatPlot, to plot cell annotation information (e.g. cluster or cell type)
spatGenePlot, to overlay (multiple) gene expression values
spatCellPlot, to overlay (multiple) numerical cell values (e.g. spatial enrichment)

3. Functions that use the dimension reduction coordinates of each cell or spot, they usually start with dimXXX

dimPlot, to plot cell annotation information (e.g. cluster or cell type)
dimGenePlot, to overlay (multiple) gene expression values
dimCellPlot, to overlay (multiple) numerical cell values (e.g. spatial enrichment)
plotPCA, plotUMAP and plotTSNE are shortcuts for dimPlot

4. Functions for co-visualization that combine spat (2) and dim (3)

spatDimPlot, to plot cell annotation information (e.g. cluster or cell type)
spatDimGenePlot, to overlay (multiple) gene expression values
spatDimCellPlot, to overlay (multiple) numerical cell values (e.g. spatial enrichment)

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 plot

see also FAQ How to create global instructions and show or save your created plots?
All parameters available to save_param are found on the help page of ?Giotto::all_plots_save_function
Hypothetical example showing a number of options:

# 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)