To visualize a given metacell partitioning by projecting metacells onto the single cell embedding space.
mcRigor_projection.RdTo visualize a given metacell partitioning by projecting metacells onto the single cell embedding space.
Usage
mcRigor_projection(
obj_singlecell,
sc_membership = NULL,
sc.reduction = c("umap", "tsne", "pca"),
dims = c(1, 2),
metric = "size",
add_testres = F,
test_stats = NULL,
Thre = NULL,
test_cutoff = 0.01,
color_field = NULL,
cpalette = c("#13678A", "#45C4B0", "#9AEBA3", "#BF847E", "#F2C12E", "#7E57C2",
"#FACFCE", "#9E9D24", "#DAFDBA", "#86ABD4", "#42A5F5", "#546E7A", "#D4E157",
"#76FF03", "#6D4C41", "#004D40", "#AB47BC", "#D81B60"),
sc.alpha = 0.5,
mc.alpha = 1,
pt_size = 1,
axis_lab = F,
max_mcsize = 1000,
continuous_metric = T,
dub_mc.label = F,
dub_mc_test.label = F,
label_text = F
)Arguments
- obj_singlecell
the Seurat object of single cells
- sc_membership
A named vector (or dataframe) of the metacell membership of single cells
- sc.reduction
The single cell reduction method to produce single cell embeddings
- dims
The dimensions to use in the single cell embeddings
- metric
The variable that determines the sizes of dots representing the metacells
- add_testres
A bool indicating whether to add the mcRigor results (dubious or trustworthy) as part of obj_metacell's metadata
- test_stats
If add_testres = True, this argument is needed. Usually should be TabMC, an output from previous steps.
- Thre
The threshold for dubious metacell detection. If not inputed, it will be computed based on test_stats.
- test_cutoff
The test size for dubious metacell detection testing
- color_field
The variable based on which to color the cells.