Dimension reduction

library(Giotto)

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1. create & process Giotto object

path_to_matrix = system.file("extdata", "seqfish_field_expr.txt", package = 'Giotto')
path_to_locations = system.file("extdata", "seqfish_field_locs.txt", package = 'Giotto')

my_giotto_object = createGiottoObject(raw_exprs = path_to_matrix,
                                      spatial_locs = path_to_locations)
my_giotto_object <- filterGiotto(gobject = my_giotto_object)
my_giotto_object <- normalizeGiotto(gobject = my_giotto_object)

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2. Highly variable genes

my_giotto_object <- calculateHVG(gobject = my_giotto_object)

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3. PCA

# run PCA
my_giotto_object <- runPCA(gobject = my_giotto_object)

# identify most informative principal components
screePlot(my_giotto_object, ncp = 20)
jackstrawPlot(my_giotto_object, ncp = 20)

# plot PCA results
plotPCA(my_giotto_object)

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4. UMAP & TSNE

# umap
my_giotto_object <- runUMAP(my_giotto_object, dimensions_to_use = 1:5)
plotUMAP(gobject = my_giotto_object)

# tsne
my_giotto_object <- runtSNE(my_giotto_object, dimensions_to_use = 1:5)
plotTSNE(gobject = my_giotto_object)