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Adjust the parameters of the APackOfTheClones reduction in a seurat object

Source: R/AdjustAPOTC.R
AdjustAPOTC.Rd

[Stable]

If the user is unsatisfied with the clonal expansion plot that was generated from RunAPOTC and APOTCPlot, this function has a range of arguments to modify the data and/or parameters of the visualization. Note that some of the arguments may conflict with eachother.

Usage

AdjustAPOTC(
  seurat_obj,
  reduction_base = NULL,
  clonecall = NULL,
  ...,
  extra_filter = NULL,
  run_id = NULL,
  new_rad_scale_factor = NULL,
  new_clone_scale_factor = NULL,
  repulse = FALSE,
  repulsion_threshold = 1,
  repulsion_strength = 1,
  max_repulsion_iter = 10L,
  relocate_cluster = NULL,
  relocation_coord = NULL,
  nudge_cluster = NULL,
  nudge_vector = NULL,
  recolor_cluster = NULL,
  new_color = NULL,
  rename_label = NULL,
  new_label = NULL,
  relocate_label = NULL,
  label_relocation_coord = NULL,
  nudge_label = NULL,
  label_nudge_vector = NULL,
  verbose = TRUE
)

Arguments

seurat_obj

The seurat object to be adjusted.

reduction_base

character. The seurat reduction to base the clonal expansion plotting on. Defaults to 'umap' but can be any reduction present within the reductions slot of the input seurat object, including custom ones. If `'pca'``, the cluster coordinates will be based on PC1 and PC2. However, generally APackOfTheClones is used for displaying UMAP and occasionally t-SNE versions to intuitively highlight clonal expansion.

clonecall

character. The column name in the seurat object metadata to use. See scRepertoire documentation for more information about this parameter that is central to both packages.

...

additional "subsetting" keyword arguments indicating the rows corresponding to elements in the seurat object metadata that should be filtered by. E.g., seurat_clusters = c(1, 9, 10) will filter the cells to those in the seurat_clusters column with any of the values 1, 9, and 10. Unfortunately, column names in the seurat object metadata cannot conflict with the keyword arguments. MAJOR NOTE if any subsetting keyword arguments are a prefix of any preceding argument names (e.g. a column named reduction is a prefix of the reduction_base argument) R will interpret it as the same argument unless both arguments are named. Additionally, this means any subsequent arguments must be named.

extra_filter

character. An additional string that should be formatted exactly like a statement one would pass into dplyr::filter that does additional filtering to cells in the seurat object - on top of the other keyword arguments - based on the metadata. This means that it will be logically AND'ed with any keyword argument filters. This is a more flexible alternative / addition to the filtering keyword arguments. For example, if one wanted to filter by the length of the amino acid sequence of TCRs, one could pass in something like extra_filter = "nchar(CTaa) - 1 > 10". When involving characters, ensure to enclose with single quotes.

run_id

character. This will be the ID associated with the data of a run, and will be used by other important functions like APOTCPlot and AdjustAPOTC. Defaults to NULL, in which case the ID will be generated in the following format:

reduction_base;clonecall;keyword_arguments;extra_filter

where if keyword arguments and extra_filter are underscore characters if there was no input for the ... and extra_filter parameters.

new_rad_scale_factor

a single numeric in (0, 1]. changes the radius scaling factor of all circles.

new_clone_scale_factor

a single numeric in (0, 1]. changes the clone_scale_factor

repulse

If TRUE, will attempt to push overlapping clusters away from each other.

repulsion_threshold

numeric. The radius that clonal circle clusters overlap is acceptable when repulsing.

repulsion_strength

numeric. The smaller the value the less the clusters repulse each other per iteration, and vice versa.

max_repulsion_iter

integer. The number of repulsion iterations.

relocate_cluster

Numeric or Character. Indicates which cluster(s) based on the index or label to relocate to new coordinates.

relocation_coord

numeric of length two or a list of numerics of length two of length of relocate_cluster. If its a list, indicates each coordinate that the clusters in relocate_cluster should move to. If its just a numeric, then will relocate all clusters in relocate_cluster to the input, which is likely not desired behavior, so this should only be convenience syntax if relocate_cluster has length 1.

nudge_cluster

Numeric or Character. Indicates which cluster(s) based on the index or label to "nudge"/translate their coordinate(s) by.

nudge_vector

numeric of length two or a list of numerics of length two of length of nudge_cluster. If its a list, indicates each translation vector (in other words, x-y coordinates) that the clusters in nudge_cluster should be translate by. If its just a numeric, then will translate all clusters in nudge_cluster by the input - which mostly is syntactic sugar for translating a single cluster if the input of nudge_cluster is of length 1.

recolor_cluster

Numeric or Character. Indicates which cluster(s) based on the index or label to change their color by.

new_color

character of arbitrary length. Indicates the corresponding new colors that selected clusters in recolor_cluster should be changed to.

rename_label

Numeric or character. Indicates the index or name of label(s) to be renamed.

new_label

Character. Indicates the corresponding new label(s) that selected label(s) in rename_label should be changed to.

relocate_label

Numeric or character. Indicates the index or name of label(s) to be relocated.

label_relocation_coord

Numeric of length two or a list of numerics of length two of length of relocate_label. If it's a list, indicates each coordinate that the labels in relocate_label should move to. If it's just a numeric, then will relocate all labels in relocate_label to the input, which is likely not desired behavior, so this should only be convenience syntax if relocate_label has length 1.

nudge_label

Numeric or character. Indicates the index or name of label(s) to be "nudged"/translated.

label_nudge_vector

Numeric of length two or a list of numerics of length two of length of nudge_label. If it's a list, indicates each translation vector (in other words, x-y coordinates) that the labels in nudge_label should be translated by. If it's just a numeric, then will translate all labels in nudge_label by the input - which mostly is syntactic sugar for translating a single label if the input of nudge_label is of length 1.

verbose

logical. Decides if visual cues are displayed to the R console of the progress.

Value

The adjusted seurat_obj

Examples

# do an APackOfTheClones run
pbmc <- RunAPOTC(get(data("combined_pbmc")), verbose = FALSE)

# adjust the rad_scale_factor, and nudge cluster 1 by x = 1, y = 1
pbmc <- AdjustAPOTC(
    pbmc,
    new_rad_scale_factor = 0.9,
    nudge_cluster = 1,
    nudge_vector = c(1, 1),
    verbose = FALSE
)
#> * using the latest APackOfTheClones Run Data with object id: umap;CTstrict;_;_

# plot the result
APOTCPlot(pbmc)
#> * using the latest APackOfTheClones Run Data with object id: umap;CTstrict;_;_
#> * generated ggplot object


# rename some labels
pbmc <- AdjustAPOTC(
    pbmc, rename_label = c(2, 5), new_label = c("Foo", "Bar")
)
#> * using the latest APackOfTheClones Run Data with object id: umap;CTstrict;_;_

# perhaps multiple clusters need to be relocated and repulsed
pbmc <- AdjustAPOTC(
    pbmc,
    relocate_cluster = c("Foo", "C10"), # using labels works too
    relocation_coord = list(c(2, 3.5), c(0, 5)),
    repulse = TRUE,
    verbose = FALSE
)
#> * using the latest APackOfTheClones Run Data with object id: umap;CTstrict;_;_

# plot again to check results
APOTCPlot(pbmc, show_labels = TRUE, verbose = FALSE)
#> * using the latest APackOfTheClones Run Data with object id: umap;CTstrict;_;_