How to Visualize and Save Plots in Giotto?#
Each Giotto function that creates a plot as 3 important parameters:
show_plot: to print the plot to the console, default is TRUE
return_plot: to return the plot as an object, default is TRUE
save_plot: to automatically save the plot, default is FALSE
These parameters are automatically provided by createGiottoObject, but can also be explicitly provided using createGiottoInstructions or a named list, which can then be given to createGiottoObject as a parameter.
Besides those 3 parameters createGiottoInstructions also allows to provide other general Giotto parameters, such as your python path and other information for automatically saving a plot, like size, plotting format, etc.
There are 4 Function To Set Instructions:
createGiottoInstructions: creates instructions that can be provided to createGiottoObject
showGiottoInstructions: to view the instructions of a Giotto object
changeGiottoInstructions: to replace 1 or more of the instruction parameters (e.g. plotting format)
replaceGiottoInstructions: to replace all instructions with new instructions (e.g after subsetting)
In addition, for each plot the parameters can always be manually overwritten within the plotting function itself.
Here we use the osmFISH as an example:
1. Create Giotto Instructions and Giotto object#
We will override automatically showing plots by setting show_plot = FALSE
We keep return_plot = TRUE, to store plots and modify them if necessary
We set save_plot = TRUE to automatically saving each plot
We also specify some other plotting parameters for the automatic saving functionality, such as the save_dir whose default is the current working directory.
library(Giotto) # create instructions for your python path, how to view your plots and # parameters to save your plot if wanted my_python_path = "/your/python/path/" # set to NULL to use previously installed giotto environment results_folder = '/path/to/your/results/' instrs = createGiottoInstructions(python_path = my_python_path, show_plot = FALSE, return_plot = TRUE, save_plot = TRUE, save_dir = results_folder, plot_format = 'png', dpi = 200, height = 9, width = 9)
2. Create Giotto Object#
Provide an expression matrix
Provide the cell locations
Provide the previously generated instructions file (named list)
## PREPARE osmFISH DATA #### # download dataset getSpatialDataset(dataset = 'osmfish_SS_cortex', directory = results_folder, method = 'wget') # path to files osm_exprs = paste0(results_folder, "osmFISH_prep_expression.txt") osm_locs = paste0(results_folder, "osmFISH_prep_cell_coordinates.txt") meta_path = paste0(results_folder, "osmFISH_prep_cell_metadata.txt") ## CREATE GIOTTO OBJECT with expression data, location data and instructions osm_test <- createGiottoObject(raw_exprs = osm_exprs, spatial_locs = osm_locs, instructions = instrs) ## add field annotation metadata = data.table::fread(file = meta_path) osm_test = addCellMetadata(osm_test, new_metadata = metadata, by_column = T, column_cell_ID = 'CellID') osm_test <- filterGiotto(gobject = osm_test) osm_test <- normalizeGiotto(gobject = osm_test)
3. Working with Giotto Instructions#
# show the provided Giotto instructions showGiottoInstructions(osm_test) # change a previously set parameter, e.g. change dpi = 200 to dpi = 300 osm_test = changeGiottoInstructions(osm_test, param = 'dpi', new_value = 300)
4. Different Ways of Saving a Plot#
Here we will show a couple of ways to save plots.
Default way according to Giotto instructions, if save_plot = TRUE (1)
Changing default parameters by by providing a named list to save_param parameter (2 & 3)
Block automatic saving, but modify the created ggplot object and save that one (4)
# 1. default instructions from Giotto object spatPlot(gobject = osm_test, cell_color = 'ClusterName') # 2. overwrite save_name instruction by providing a named list for save_param # save_param takes all parameters of all_plots_save_function spatPlot(gobject = osm_test, cell_color = 'ClusterName', save_param = list(save_name = 'myplot')) # 3. overwrite save_name instruction and add specific subfolder # save_folder creates a specific subfolder in the provided directory spatPlot(gobject = osm_test, cell_color = 'ClusterName', point_size = 1.5, save_param = list(save_folder = '2_Gobject', save_name = 'original_clusters', units = 'in', base_height = 6, base_width = 6)) # 4. do not save, but return as object, modify and save # for example to create a black background: # we can change the parameter 'background_color' to black in the spatPlot function # OR return the ggplot object and change the panel.background to black within theme mypl = spatPlot(gobject = osm_test, cell_color = 'ClusterName', save_plot = F) mypl = mypl + theme(panel.background = element_rect(fill ='black'), panel.grid = element_blank()) mypl = mypl + guides(fill = guide_legend(override.aes = list(size=5))) mypl # save in specified folder gobject_folder = paste0(results_folder,'/','2_Gobject/') if(!file.exists(gobject_folder)) dir.create(gobject_folder, recursive = T) cowplot::save_plot(plot = mypl, filename = 'original_clusters_black.png', path = gobject_folder, device = png(), dpi = 300, base_height = 10, base_width = 10)