R/S4-documentation.R
In kueckelj/SPATA2: A Toolbox for Spatial Gene Expression Analysis
# miscellaneous -----------------------------------------------------------
# 0 - classes on which other classes depend on ----------------------------
#' @title The \code{Trajectory} - Class
#'
#' @description S4 class that represents trajectories
#' drawn within real or latent space.
#'
#' @slot comment character. A comment about why the trajectory was drawn.
#' @slot id character. ID that uniquely identfies the trajectory in a sample.
#' @slot projection data.frame. Data.frame that contains the length of the
#' projection of each barcode spot onto the trajectory.
#' @slot sample character. The sample name.
#' @slot segment data.frame. Contains the course of the trajetory in
#' form of a data.frame with the variables \emph{x, y, xend} and \emph{yend.}
#' @slot width numeric. The width of the rectangle that was spanned along
#' the trajectory. (Length of the rectangle corresponds to the length of
#' the segment.)
#'
#' @export
Trajectory <- setClass(Class = "Trajectory",
slots = list(
comment = "character",
id = "character",
projection = "data.frame",
sample = "character",
segment = "data.frame",
width = "numeric"
))
# H -----------------------------------------------------------------------
image_class <- "Image"
base::attr(x = image_class, which = "package") <- "EBImage"
#' @title The \code{HistologyImaging} - Class
#'
#' @description S4 class that represents a set of histological images from one
#' and the same tissue slide.
#'
#' @slot annotations list. List of objects of class \code{ImageAnnotation}.
#' @slot coordinates data.frame. A data.frame of observational units that underlie
#' the image in case of spatially resolved multi-omic studies. Should contain at least
#' the two variables: *x*, *y* and a variable that identifies the observational
#' units (e.g. *barcodes*).
#' @slot dir_add list. Named list of directories that contain different versions
#' of tissue images. Can be arbitrarily expanded for convenient exchanging via
#' `loadImage()`.
#' @slot dir_default character. Directory that leads to the default image for save
#' exchanging via `loadDefaultImage()`.
#' @slot dir_highres character. Directory that leads to a high resolution version of the image
#' for save exchanging via `loadHighresImage()`.
#' @slot dir_lowres character. Directory that leads to a low resolution version of the image
#' for save exchanging via `loadLowresImage()`.
#' @slot grid list. That contains information about spatial grids.
#' @slot id character. String to identify the imaged tissue.
#' @slot image Image. Should be compatible with the `EBImage` package.
#' @slot image_info list. Stores meta data and miscellaneous information regarding the
#' image that is currently stored in slot @@image. Slots that should always exist:
#' \itemize{
#' \item{*origin*:}{ Character string. Either the directory from where the current image was read
#' in or a substitute of the object name that was used from the global environment.}
#' \item{*dim_input*:}{ The dimensions with which the image was given to argument `image` of
#' `createHistologyImaging()` or `exchangeImage()`.}
#' \item{*dim_stored*:}{ The dimensions with which the image is currently stored.}
#' \item{*img_scale_fct*:}{ The scale factor input that was used to resize the current image within
#' `createHistologyImaging()` or `exchangeImage()` before setting it. If 1, *dim_stored* and *dim_input*
#' should be identical. See argument `scale_fct` of `exchangeImage()` for more details on its interpretation.}
#' \item{*pxl_scale_fct*:}{ Numeric value that gives the side length of one pixel an SI unit that is stated
#' in an attribute called *unit* as nSI-units/px.}
#' }
#' @slot justification list. List of two slots that track justification changes. See corresponding
#' section below the slot descriptions for more information.
#' \itemize{
#' \item{*angle*:}{ Numeric value that ranges from 0-359.}
#' \item{*flipped*:}{ List of two logical values named *horizontal* and *vertical*.}
#' }
#' @slot meta list. List for meta data regarding the tissue.
#' @slot misc list. A flexible list for miscellaneous input.
#'
#' @section Requirements:
#' The `HistologyImaging` framework assumes that all read in images have the same
#' axes-ratio.
#'
#' @section Tracking changes in image justification:
#' The histology image that is used while creating the object is considered the
#' default image. By default, the framework assumes that all related images (high resolution,
#' low resolution, fluorescent images, RAMAN spectroscopy etc.) have the same justification
#' in terms of angle rotation and axes-flipping. Flipping an image in the `SPATA2` object via
#' `flipImage()` or rotating images via `rotateImage()` changes their justification in space.
#' These changes in justification are tracked (if `track` is not set to `FALSE`) and applied
#' whenever an image is exchanged via `exchangeImage()` (if `adjust` is not set to `FALSE`).
#' This ensures consistent image exchanges using the different directories.
#'
#' @export
HistologyImaging <- setClass(Class = "HistologyImaging",
slots = list(
annotations = "list",
coordinates = "data.frame",
dir_default = "character",
dir_highres = "character",
dir_lowres = "character",
dir_add = "list",
grid = "list",
id = "character",
image = image_class,
image_info = "list",
justification = "list",
meta = "list",
misc = "list"
)
)
# I -----------------------------------------------------------------------
#' @title The \code{ImageAnnotation} - Class
#'
#' @description S4 class that represents manually annotated structures in
#' histology images.
#'
#' @slot area list. A named list of data.frames with the numeric variables \emph{x} and \emph{y}.
#' Observations correspond to the vertices of the polygons that are needed to represent the
#' image annotation. **Must** contain a slot named *outer* which sets the outer border
#' of the image annotation. **Can** contain multiple slots named *inner* (suffixed)
#' with numbers that correspond to inner polygons - holes within the annotation.
#' @slot id character. String to identify the object in a list of multiple objects
#' of the same class.
#' @slot image image. Cropped version of the annotated parent image that only contains
#' the area where the annotated structure is located (plus expand). This slot should
#' be empty as long as the \code{ImageAnnotation} object is located in an
#' object of class \code{HistologyImaging}. Extracting it with \code{getImageAnnotation()}
#' or \code{getImageAnnotations()} can add a cropped image to the slot. The parameters
#' with which the image was cropped should be in the list of slot @@image_info.
#' @slot image_info list. List of information around the image that is currently
#' stored in slot @@image after being cropped and set within \code{getImageAnnotation()}
#' or \code{getImageAnnotations()}.
#' @slot info list. Stores meta data and miscellaneous information regarding the
#' image annotation. Slots that should always exist:
#' \itemize{
#' \item{parent_origin:}{ Character string. Content from slot @@info$origin of the `HistologyImaging`
#' object the annotation belongs to. Identifies the exact image on which the annotation was drawn in.}
#' \item{parent_id:}{ Character string. Content from slot @@id of the `HistologyImaging`
#' object the annotation belongs to. Identifies the `HistologyImaging` object (the tissue) the annotation
#' belongs to.}
#' \item{current_dim:}{ Numeric vector of length two. Width and height of the image
#' the @@area data.frame is currently scaled to. Used to scale the @@area data.frame
#' if the image annotation is extracted and added to a `SPATA2` object with different image resolution.}
#' \item{current_just:}{ List of two slots that track justification changes. Is used to readjust the
#' @@area data.frame if the image annotation is extracted and added to a `SPATA2` object with
#' different justifications.
#' \itemize{
#' \item{*angle*:}{ Numeric value that ranges from 0-359.}
#' \item{*flipped*:}{ List of two logical values named *horizontal* and *vertical*.}
#' }}
#' }
#' @slot misc list. A flexible list for miscellaneous input.
#' @slot tags character. Vector of arbitrary length. Contains tags that can be used
#' to group and select image annotations in different manners.
#'
#' @section Image annotation tags:
#' Slot @@tags contains a character vector of arbitrary length that allows
#' to filter image annotations using a combination of arguments `tags` and
#' `test` in functions that refer to one or more image annotations like
#' `getImageAnnotations()` or `plotImageAnnotations()`.
#'
#' Input for argument \code{tags} specifies the tags of interest.
#' Argument \code{test} decides about how the specified tags are used to select
#' the image annotations of interest. There are multiple options:
#'
#' 1. Argument \code{test} set to \emph{'any'} or \emph{1}: To be included, an image annotation
#' must be tagged with at least one of the input tags.
#'
#' 2. Argument \code{test} set to \emph{'all'} or \emph{2}: To be included, an image annotation
#' must be tagged with all of the input tags. Can contain tags that are not specified.
#'
#' 3. Argument \code{test} set to \emph{'identical'} or \emph{3}: To be included, an image annotation
#' must be tagged with all of the input tags. Can not be tagged with anything else.
#'
#' 4. Argument `test` set to *not_identical* or *4*: To be included, an image
#' annotation must **not** be tagged with the combination of input tags.
#'
#' 5. Argument `test` set to *'none'* or *5*: To be included, an image annotation
#' must **not** contain any of the input tags.
#'
#' Note that the filtering process happens in addition to / after the filtering by input for argument
#' \code{ids}.
#'
#' @export
#'
ImageAnnotation <- setClass(Class = "ImageAnnotation",
slots = list(
area = "list",
id = "character",
image = image_class,
image_info = "list",
info = "list",
misc = "list",
tags = "character"
)
)
#' @title The \code{ImageAnnotationScreening} - Class
#'
#' @description S4 class that contains input for and output of the
#' function \code{imageAnnotationScreening()}.
#'
#' @slot angle_span numeric. Vector of length two. Confines the area of interest
#' by angle relative to the center of the image annotation.
#' @slot binwidth numeric. The value with which the polygon that encircles
#' the image annotation is consecutively expanded via \code{sf::st_buffer()},
#' @slot coords data.frame. Coordinates data.frame of the sample.
#' @slot img_annotation ImageAnnotation. The \code{ImageAnnotation}-object of
#' the image annotation chosen for the screening.
#' @slot info list. Miscellaneous information.
#' @slot method_padj character. The method with which p-values were adjusted.
#' @slot models data.frame. The model data.frame that has been used for the
#' screening.
#' @slot n_bins_angle numeric. Number of bins that were created anglewise.
#' @slot n_bins_circle numeric. Number of bins that were created circlewise.
#' @slot results_primary data.frame. Data.frame that contains the results of
#' the model fitting per angle bin.
#' @slot results data.frame. Data.frame that contains the summary of
#' all gene-model fits across all angle bins.
#' @slot sample character. The sample name.
#' @slot summarize_with character. Either \emph{'mean'} or \emph{'median'}.
#'
#' @export
#'
ImageAnnotationScreening <- setClass(Class = "ImageAnnotationScreening",
slots = list(
angle_span = "numeric",
binwidth = "numeric",
coords = "data.frame",
distance = "numeric",
img_annotation = "ImageAnnotation",
info = "list",
method_padj = "character",
models = "data.frame",
n_bins_angle = "numeric",
n_bins_circle = "numeric",
results_primary = "data.frame",
results = "data.frame",
sample = "character",
summarize_with = "character",
bcsp_exclude = "character"
))
# S -----------------------------------------------------------------------
#' @title The `spata2`- Class
#'
#' @slot autoencoder A list in which the results of neural network denoising is stored.
#'
#' @slot coordinates A data.frame containing information about every barcode-spot. Must contain the variables:
#'
#' \describe{
#' \item{\emph{barcodes}}{Character. The barcode-sequences (+ the sample belonging) of every barcode spot.}
#' \item{\emph{sample}}{Character. The sample belonging of every barcode-spot.}
#' \item{\emph{x}}{Numeric. The x-coordinates of every barcode.}
#' \item{\emph{y}}{Numeric. The y-coordinates of every barcode.}
#' }
#'
#' @slot data See documentation for S4-object 'data'
#' @slot dea A list in which every slot is named according to a discrete feature for which differential gene expression
#' analysis has been conducted (via \code{findDeGenes()}). Every slot contains a data.frame (output of \code{Seurat::FindAllMarkers()}).
#' @slot dim_red See documentation for S4-object 'dim_red'
#' @slot fdata A data.frame containing the additionally computed features. Must contain the variables:
#' \describe{
#' \item{\emph{barcodes}}{Character. The barcode-sequences (+ the sample belonging) of every barcode spot.}
#' \item{\emph{sample}}{Character. The sample belonging of every barcode-spot.}
#' }
#'
#' @slot image A list of images named according to the samples the object contains.
#' @slot samples Character value. Contains the sample names.
#' @slot scvelo Currently not in use.
#' @slot trajectories A list named according to the samples the object contains. Each slot in
#' that list contains another list of all 'spatial_trajectory'-objects created for that sample.
#'
#' @slot used_genesets A data.frame containing the defined gene-sets. Must contain the variables:
#'
#' \describe{
#' \item{\emph{ont}}{Character. The gene-set name.}
#' \item{\emph{gene}}{Character. The belonging genes.}
#' }
#'
#' @slot version A list of four slots denoting the version of SPATA under which the object has been
#' created.
#'
#' @slot compatibility A list of miscellaneous information that mainly ensures compatibility between different
#' platforms.
#'
#' @return S4 object
#' @export
spata2 <- setClass("spata2",
slots = c(autoencoder = "list",
cnv = "list",
compatibility = "list",
coordinates ="list", #coordinates: bc, x, y, sample
data = "list",
dea = "list",
dim_red = "list", #PCA, UMAP, TSNE: bc, umap1, umap2, sample
fdata = "list", #fdata : bc, ...
gdata = "list",
images = "list",
information = "list",
samples = "character",
spatial = "list",
scvelo = "list",
trajectories = "list",
used_genesets = "data.frame",
version = "list")
)
#' @title The \code{SpatialMethod} - Class
#'
#' @description Abstracts the concept of spatial biology experiments
#' such as \emph{Visium1} or \emph{SlideSeq}.
#'
#' @slot fiducial_frame list. List of length two or three. Provides
#' standardized measures of the sample image in units of length.
#' @slot info list. List of miscellaneous meta data for the method.
#' @slot name character. The name of the spatial method. Should
#' be one of \code{validSpatialMethods()}.
#' @slot observational_unit character. Single word that describes
#' the observational unit of the experiment. E.g \emph{'barcode-spot'} in
#' case of @@name == \emph{'Visium'}.
#'
#' @export
SpatialMethod <- setClass(Class = "SpatialMethod",
slots = list(
fiducial_frame = "list",
info = "list",
name = "character",
unit = "character",
observational_unit = "character"
))
#' @title The `SpatialSegmentation` - Class
#'
#' @description Abstracts the concept of manual segmentation/annotation
#' of the sample surface.
#'
#' @slot id character. String to identify the object in a list of multiple objects of
#' the same class.
#'
#' @slot info list. Stores meta data and miscellaneous information regarding the
#' spatial segmentation. Slots that should always exist:
#' \itemize{
#' \item{sample:}{ Character string. The name of the sample (slot @@sample of the `SPATA2` object.)}
#' }
#'
#' @slot segments list. A named, nested list. Named according to the labels
#' given to each segment. E.g. list of length two with slot *necrosis* and *vivid*.
#' Each named slot is a unnamed list. In this list each slot is a list of data.frames with
#' a *x* and a *y* variable. First data.frame, named *exterior* corresponds to the exterior border of
#' the segment. Every following data.frame is named *interior*-suffix where the suffix is a number
#' and corresponds to interior holes of the segment.
#'
#' @keywords internal
#'
SpatialSegmentation <- setClass(Class = "SpatialSegmentation",
slots = list(
id = "character",
info = "list",
segments = "list"
))
#' @title The `SpatialSegment` - Class
#'
#' @description Abstracts the concept of an annotated segment within a spatial
#' segmentation.
#'
#' @slot info list. Stores meta data and miscellaneous information regarding the
#' spatial segment. Slots that should always exist:
#' \itemize{
#' \item{image_origin:}{ Character string. Content of slot @@info$origin of the `HistologyImaging` at the
#' time the segment was drawn.}
#' \item{parent_id:}{ Character string. The ID of the spatial segmentation this segment is part of.}
#' \item{pot:}{ POSIXct. The point of time when the segment was drawn. Used to handle overlapping
#' segments.}
#' \item{sample:}{ Character string. The name of the sample (slot @@sample of the `SPATA2` object.)}
#' }
#' @slot label character. Character string. The label that was given to the segment.
#' Corresponds to the group name of the barcode-spots that fall into the segment.
#' @slot polygons list. List of data.frames with *x* and *y* variables that contain
#' the vertices of the polygon. The first polygon (should be named *outer*) defines
#' the outer ring of the segment. Further polygons (should be named *inner* suffixed
#' with a number) define holes within the segment.
#'
#' @keywords internal
SpatialSegment <- setClass(Class = "SpatialSegment",
slots = list(
info = "list",
label = "character",
polygons = "list"
))
#' @title The \code{SpatialTrajectory} - Class
#'
#' @description Extension of the \code{Trajectory} for trajectories
#' that have been drawn on a surface plot.
#'
#' @slot comment character. A comment about why the trajectory was drawn.
#' @slot coords data.frame. The coordinates data.frame of the sample.
#' @slot id character. ID that uniquely identfies the trajectory in a sample.
#' @slot info list. Stores meta data and miscellaneous information regarding the
#' image annotation. Slots that should always exist:
#' \itemize{
#' \item{current_dim:}{ Numeric vector of length two. Width and height of the image
#' the @@area data.frame is currently scaled to. Used to scale the @@area data.frame
#' if the image annotation is extracted and added to a `SPATA2` object with different image resolution.}
#' \item{current_just:}{ List of two slots that track justification changes. Is used to readjust the
#' @@area data.frame if the image annotation is extracted and added to a `SPATA2` object with
#' different justifications.
#' \itemize{
#' \item{*angle*:}{ Numeric value that ranges from 0-359.}
#' \item{*flipped*:}{ List of two logical values named *horizontal* and *vertical*.}
#' }}
#' }
#' @slot projection data.frame. Data.frame that contains the length of the
#' projection of each barcode spot onto the trajectory.
#' @slot sample character. The sample name.
#' @slot segment data.frame. Contains the course of the trajetory in
#' form of a data.frame with the variables \emph{x, y, xend} and \emph{yend.}
#' @slot width numeric. The width of the rectangle that was spanned along
#' the trajectory. (Length of the rectangle corresponds to the length of
#' the segment.)
#' @slot with_unit character. The unit in which the width was specified.
#' @export
SpatialTrajectory <- setClass(Class = "SpatialTrajectory",
slots = list(
coords = "data.frame",
info = "list",
width_unit = "character"
),
contains = "Trajectory")
#' @title The \code{SpatialTrajectoryScreening} - class
#'
#' @description S4 class that contains input for and output of the
#' function \code{spatialTrajectoryScreening()}.
#'
#' @slot binwidth numeric. The width of the bins in which the barcode-spots
#' are put based on the projection length values.
#' @slot coords data.frame. Coordinates data.frame of the sample.
#' @slot id character. The ID of the screened trajectory.
#' @slot method_padj character. The method with which p-values were adjusted.
#' @slot models data.frame. The model data.frame that has been used for the
#' screening.
#' @slot n_bins numeric. The number of bins in which the barcode-spots
#' are distributed based on their projection length.
#' @slot results data.frame. A data.frame that contains the model evaluations
#' @slot sample character. The sample name.
#' @slot summarize_with character. The name of the function that has been
#' used to summarize the variables by bin.
#' @slot spatial_trajectory SpatialTrajectory. The spatial trajectory based on
#' which the screening took place.
#'
#' @export
#'
SpatialTrajectoryScreening <- setClass(Class = "SpatialTrajectoryScreening",
slots = list(
binwidth = "numeric",
coords = "data.frame",
id = "character",
method_padj = "character",
models = "data.frame",
n_bins = "numeric",
results = "data.frame",
sample = "character",
summarize_with = "character",
spatial_trajectory = "SpatialTrajectory"
))
# T -----------------------------------------------------------------------
# Trajectory - other S4 classes inherit from it. Is listed on top under 0
#' @title The \code{Visium} - Class
#'
#' @description Abstracts the concept of 10X Visium spatial biology experiments.
#'
#' @slot capture_area list. List of length two. Provides
#' standardized measures of the active region where tissue can
#' be placed on a Visium slide.
#' @slot ccd character. The center to center distance
#' of the barcoded spots provided in a valid `SPATA2` spatial measure.
#' @slot fiducial_frame list. List of length two. Provides
#' standardized measures of spots help the sample microscopist see where
#' to place tissue and are also used by Space Ranger to determine
#' where the capture area is in an image.
#' @slot info list. List of miscellaneous meta data for the method.
#' @slot name character. The name of the spatial method.
#' @slot observational_unit character. Single word that describes
#' the observational unit of the experiment.
#'
#' @inheritSection section_dummy Distance measures
#'
#' @export
Visium <- setClass(Class = "Visium",
contains = "SpatialMethod",
slots = list(
capture_area = "list",
ccd = "character",
fiducial_frame = "list"
)
)
# Deprecated --------------------------------------------------------------
#' data_counts object
#'
#' @slot counts A sparse matrix containing the original counts.
#' @slot norm_exp A processed expression matrix. Rownames must be the gene-names.
#' Column names must be the barcodes.
#'
#' @return S4 object
#' @export
#' @keywords internal
data_counts <- setClass("data_counts",
slots = c(counts = "Matrix",
norm_exp = "matrix"))
#' dim_red object
#'
#' @slot UMAP A data.frame containing the variables \emph{'barcdoes', 'sample', 'umap1', 'umap2'}
#' @slot TSNE A data.frame containing the variables \emph{'barcodes', 'smaple', 'tsne1', 'tsne2'}
#'
#' @return S4 object
#' @export
#' @keywords internal
dim_red <- setClass("dim_red",
slots = c(UMAP = "data.frame",
TSNE ="data.frame"))
#' @title The \code{HistologyImage} - Class
#'
#' @description S4 class that represents histology images.
#'
#' @slot annotations list. List of objects of class \code{ImageAnnotation}.
#' @slot dir_default character. The default directory that is used to load
#' the image if slot @@image is empty. Or a string linking to the default slot
#' ('highres' or 'lowres').
#' @slot dir_highres character. Directory to the high resolution version of the image.
#' @slot dir_lowres character. Directory to the low resolution version of the image.
#' @slot grid data.frame. A data.frame that contains at least a variable
#' named \emph{x} and a variable named \emph{y} representing a grid.
#' @slot id character. String to identify the object in a list of multiple objects
#' of the same class. Usually refers to the sample name of the \code{SPATA2} object.
#' @slot image Image.
#' @slot info list. A flexible list that is supposed to store miscellaneous
#' information around the image.
#' @slot misc list. A flexible list for miscellaneous input.
#' @keywords internal
#' @export
HistologyImage <- setClass(Class = "HistologyImage",
slots = list(
annotations = "list",
coordinates = "data.frame",
dir_default = "character",
dir_highres = "character",
dir_lowres = "character",
grid = "list",
id = "character",
info = "list",
image = image_class,
misc = "list"
))
#' spatial_trajectory object
#'
#' @slot compiled_trajectory_df A data.frame containing the variables:
#'
#' \describe{
#' \item{\emph{barcodes}}{Character. The barcode-spots' sequences.}
#' \item{\emph{sample}}{Character. The barcode-spots' sample belonging.}
#' \item{\emph{x,y}}{Numeric. The barcode-spots' spatial coordinates.}
#' \item{\emph{projection_length}}{Numeric. The distance between the barcode-spots'
#' projection onto the trajectory-vector and the start of the trajectory.}
#' \item{\emph{trajectory_part}}{Character. The part of the trajectory.}
#' }
#'
#'
#' @slot segment_trajectory_df A data.frame containing the numeric variables
#' \emph{x, y, xend, yend} that denote the start and the end of every trajectory
#' part.
#' @slot comment Character value. The comment written down before saving the trajectory.
#' @slot name Character value. The trajectory's name.
#' @slot sample Character value. The sample the trajectory belongs to.
#'
#' @return S4 object
#' @export
#' @keywords internal
spatial_trajectory <- setClass("spatial_trajectory",
slots = c(
compiled_trajectory_df = "data.frame",
segment_trajectory_df = "data.frame",
comment = "character",
name = "character",
sample = "character"))
#' default instructions
#' @export
#' @keywords internal
default_instructions <- setClass(Class = "default_instructions",
slots = c(
average_genes = "logical",
binwidth = "numeric",
clrp = "character",
clrsp = "character",
colors = "character",
complete = "logical",
concavity = "numeric",
display_facets = "logical",
display_image = "logical",
display_labels = "logical",
display_legend = "logical",
display_points = "logical",
display_residuals = "logical",
display_trajectory_parts = "logical",
display_title = "logical",
expand_outline = "numeric",
max_adj_pval = "numeric",
method_aggl = "character",
method_dist = "character",
method_de = "character",
method_dr = "character",
method_hclust = "character",
method_ovl = "character",
method_padj = "character",
method_gs = "character",
min_lfc = "numeric",
n_highest_lfc = "numeric",
n_lowest_pval = "numeric",
n_pcs = "numeric",
normalize = "logical",
position = "character",
pt_alpha = "numeric",
pt_clr = "character",
pt_clrp = "character",
pt_clrsp = "character",
pt_fill = "character",
pt_shape = "numeric",
pt_size = "numeric",
pt_size_fixed = "logical",
relevel = "logical",
scales = "character",
sgmt_clr = "character",
sgmt_size = "numeric",
show_colnames = "logical",
show_rownames = "logical",
smooth = "logical",
smooth_clr = "character",
smooth_method = "character",
smooth_se = "logical",
smooth_span = "numeric",
uniform_genes = "character",
verbose = "logical")
)
kueckelj/SPATA2 documentation built on March 16, 2024, 10:25 a.m.
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# miscellaneous -----------------------------------------------------------
# 0 - classes on which other classes depend on ----------------------------
#' @title The \code{Trajectory} - Class
#'
#' @description S4 class that represents trajectories
#' drawn within real or latent space.
#'
#' @slot comment character. A comment about why the trajectory was drawn.
#' @slot id character. ID that uniquely identfies the trajectory in a sample.
#' @slot projection data.frame. Data.frame that contains the length of the
#' projection of each barcode spot onto the trajectory.
#' @slot sample character. The sample name.
#' @slot segment data.frame. Contains the course of the trajetory in
#' form of a data.frame with the variables \emph{x, y, xend} and \emph{yend.}
#' @slot width numeric. The width of the rectangle that was spanned along
#' the trajectory. (Length of the rectangle corresponds to the length of
#' the segment.)
#'
#' @export
Trajectory <- setClass(Class = "Trajectory",
slots = list(
comment = "character",
id = "character",
projection = "data.frame",
sample = "character",
segment = "data.frame",
width = "numeric"
))
# H -----------------------------------------------------------------------
image_class <- "Image"
base::attr(x = image_class, which = "package") <- "EBImage"
#' @title The \code{HistologyImaging} - Class
#'
#' @description S4 class that represents a set of histological images from one
#' and the same tissue slide.
#'
#' @slot annotations list. List of objects of class \code{ImageAnnotation}.
#' @slot coordinates data.frame. A data.frame of observational units that underlie
#' the image in case of spatially resolved multi-omic studies. Should contain at least
#' the two variables: *x*, *y* and a variable that identifies the observational
#' units (e.g. *barcodes*).
#' @slot dir_add list. Named list of directories that contain different versions
#' of tissue images. Can be arbitrarily expanded for convenient exchanging via
#' `loadImage()`.
#' @slot dir_default character. Directory that leads to the default image for save
#' exchanging via `loadDefaultImage()`.
#' @slot dir_highres character. Directory that leads to a high resolution version of the image
#' for save exchanging via `loadHighresImage()`.
#' @slot dir_lowres character. Directory that leads to a low resolution version of the image
#' for save exchanging via `loadLowresImage()`.
#' @slot grid list. That contains information about spatial grids.
#' @slot id character. String to identify the imaged tissue.
#' @slot image Image. Should be compatible with the `EBImage` package.
#' @slot image_info list. Stores meta data and miscellaneous information regarding the
#' image that is currently stored in slot @@image. Slots that should always exist:
#' \itemize{
#' \item{*origin*:}{ Character string. Either the directory from where the current image was read
#' in or a substitute of the object name that was used from the global environment.}
#' \item{*dim_input*:}{ The dimensions with which the image was given to argument `image` of
#' `createHistologyImaging()` or `exchangeImage()`.}
#' \item{*dim_stored*:}{ The dimensions with which the image is currently stored.}
#' \item{*img_scale_fct*:}{ The scale factor input that was used to resize the current image within
#' `createHistologyImaging()` or `exchangeImage()` before setting it. If 1, *dim_stored* and *dim_input*
#' should be identical. See argument `scale_fct` of `exchangeImage()` for more details on its interpretation.}
#' \item{*pxl_scale_fct*:}{ Numeric value that gives the side length of one pixel an SI unit that is stated
#' in an attribute called *unit* as nSI-units/px.}
#' }
#' @slot justification list. List of two slots that track justification changes. See corresponding
#' section below the slot descriptions for more information.
#' \itemize{
#' \item{*angle*:}{ Numeric value that ranges from 0-359.}
#' \item{*flipped*:}{ List of two logical values named *horizontal* and *vertical*.}
#' }
#' @slot meta list. List for meta data regarding the tissue.
#' @slot misc list. A flexible list for miscellaneous input.
#'
#' @section Requirements:
#' The `HistologyImaging` framework assumes that all read in images have the same
#' axes-ratio.
#'
#' @section Tracking changes in image justification:
#' The histology image that is used while creating the object is considered the
#' default image. By default, the framework assumes that all related images (high resolution,
#' low resolution, fluorescent images, RAMAN spectroscopy etc.) have the same justification
#' in terms of angle rotation and axes-flipping. Flipping an image in the `SPATA2` object via
#' `flipImage()` or rotating images via `rotateImage()` changes their justification in space.
#' These changes in justification are tracked (if `track` is not set to `FALSE`) and applied
#' whenever an image is exchanged via `exchangeImage()` (if `adjust` is not set to `FALSE`).
#' This ensures consistent image exchanges using the different directories.
#'
#' @export
HistologyImaging <- setClass(Class = "HistologyImaging",
slots = list(
annotations = "list",
coordinates = "data.frame",
dir_default = "character",
dir_highres = "character",
dir_lowres = "character",
dir_add = "list",
grid = "list",
id = "character",
image = image_class,
image_info = "list",
justification = "list",
meta = "list",
misc = "list"
)
)
# I -----------------------------------------------------------------------
#' @title The \code{ImageAnnotation} - Class
#'
#' @description S4 class that represents manually annotated structures in
#' histology images.
#'
#' @slot area list. A named list of data.frames with the numeric variables \emph{x} and \emph{y}.
#' Observations correspond to the vertices of the polygons that are needed to represent the
#' image annotation. **Must** contain a slot named *outer* which sets the outer border
#' of the image annotation. **Can** contain multiple slots named *inner* (suffixed)
#' with numbers that correspond to inner polygons - holes within the annotation.
#' @slot id character. String to identify the object in a list of multiple objects
#' of the same class.
#' @slot image image. Cropped version of the annotated parent image that only contains
#' the area where the annotated structure is located (plus expand). This slot should
#' be empty as long as the \code{ImageAnnotation} object is located in an
#' object of class \code{HistologyImaging}. Extracting it with \code{getImageAnnotation()}
#' or \code{getImageAnnotations()} can add a cropped image to the slot. The parameters
#' with which the image was cropped should be in the list of slot @@image_info.
#' @slot image_info list. List of information around the image that is currently
#' stored in slot @@image after being cropped and set within \code{getImageAnnotation()}
#' or \code{getImageAnnotations()}.
#' @slot info list. Stores meta data and miscellaneous information regarding the
#' image annotation. Slots that should always exist:
#' \itemize{
#' \item{parent_origin:}{ Character string. Content from slot @@info$origin of the `HistologyImaging`
#' object the annotation belongs to. Identifies the exact image on which the annotation was drawn in.}
#' \item{parent_id:}{ Character string. Content from slot @@id of the `HistologyImaging`
#' object the annotation belongs to. Identifies the `HistologyImaging` object (the tissue) the annotation
#' belongs to.}
#' \item{current_dim:}{ Numeric vector of length two. Width and height of the image
#' the @@area data.frame is currently scaled to. Used to scale the @@area data.frame
#' if the image annotation is extracted and added to a `SPATA2` object with different image resolution.}
#' \item{current_just:}{ List of two slots that track justification changes. Is used to readjust the
#' @@area data.frame if the image annotation is extracted and added to a `SPATA2` object with
#' different justifications.
#' \itemize{
#' \item{*angle*:}{ Numeric value that ranges from 0-359.}
#' \item{*flipped*:}{ List of two logical values named *horizontal* and *vertical*.}
#' }}
#' }
#' @slot misc list. A flexible list for miscellaneous input.
#' @slot tags character. Vector of arbitrary length. Contains tags that can be used
#' to group and select image annotations in different manners.
#'
#' @section Image annotation tags:
#' Slot @@tags contains a character vector of arbitrary length that allows
#' to filter image annotations using a combination of arguments `tags` and
#' `test` in functions that refer to one or more image annotations like
#' `getImageAnnotations()` or `plotImageAnnotations()`.
#'
#' Input for argument \code{tags} specifies the tags of interest.
#' Argument \code{test} decides about how the specified tags are used to select
#' the image annotations of interest. There are multiple options:
#'
#' 1. Argument \code{test} set to \emph{'any'} or \emph{1}: To be included, an image annotation
#' must be tagged with at least one of the input tags.
#'
#' 2. Argument \code{test} set to \emph{'all'} or \emph{2}: To be included, an image annotation
#' must be tagged with all of the input tags. Can contain tags that are not specified.
#'
#' 3. Argument \code{test} set to \emph{'identical'} or \emph{3}: To be included, an image annotation
#' must be tagged with all of the input tags. Can not be tagged with anything else.
#'
#' 4. Argument `test` set to *not_identical* or *4*: To be included, an image
#' annotation must **not** be tagged with the combination of input tags.
#'
#' 5. Argument `test` set to *'none'* or *5*: To be included, an image annotation
#' must **not** contain any of the input tags.
#'
#' Note that the filtering process happens in addition to / after the filtering by input for argument
#' \code{ids}.
#'
#' @export
#'
ImageAnnotation <- setClass(Class = "ImageAnnotation",
slots = list(
area = "list",
id = "character",
image = image_class,
image_info = "list",
info = "list",
misc = "list",
tags = "character"
)
)
#' @title The \code{ImageAnnotationScreening} - Class
#'
#' @description S4 class that contains input for and output of the
#' function \code{imageAnnotationScreening()}.
#'
#' @slot angle_span numeric. Vector of length two. Confines the area of interest
#' by angle relative to the center of the image annotation.
#' @slot binwidth numeric. The value with which the polygon that encircles
#' the image annotation is consecutively expanded via \code{sf::st_buffer()},
#' @slot coords data.frame. Coordinates data.frame of the sample.
#' @slot img_annotation ImageAnnotation. The \code{ImageAnnotation}-object of
#' the image annotation chosen for the screening.
#' @slot info list. Miscellaneous information.
#' @slot method_padj character. The method with which p-values were adjusted.
#' @slot models data.frame. The model data.frame that has been used for the
#' screening.
#' @slot n_bins_angle numeric. Number of bins that were created anglewise.
#' @slot n_bins_circle numeric. Number of bins that were created circlewise.
#' @slot results_primary data.frame. Data.frame that contains the results of
#' the model fitting per angle bin.
#' @slot results data.frame. Data.frame that contains the summary of
#' all gene-model fits across all angle bins.
#' @slot sample character. The sample name.
#' @slot summarize_with character. Either \emph{'mean'} or \emph{'median'}.
#'
#' @export
#'
ImageAnnotationScreening <- setClass(Class = "ImageAnnotationScreening",
slots = list(
angle_span = "numeric",
binwidth = "numeric",
coords = "data.frame",
distance = "numeric",
img_annotation = "ImageAnnotation",
info = "list",
method_padj = "character",
models = "data.frame",
n_bins_angle = "numeric",
n_bins_circle = "numeric",
results_primary = "data.frame",
results = "data.frame",
sample = "character",
summarize_with = "character",
bcsp_exclude = "character"
))
# S -----------------------------------------------------------------------
#' @title The `spata2`- Class
#'
#' @slot autoencoder A list in which the results of neural network denoising is stored.
#'
#' @slot coordinates A data.frame containing information about every barcode-spot. Must contain the variables:
#'
#' \describe{
#' \item{\emph{barcodes}}{Character. The barcode-sequences (+ the sample belonging) of every barcode spot.}
#' \item{\emph{sample}}{Character. The sample belonging of every barcode-spot.}
#' \item{\emph{x}}{Numeric. The x-coordinates of every barcode.}
#' \item{\emph{y}}{Numeric. The y-coordinates of every barcode.}
#' }
#'
#' @slot data See documentation for S4-object 'data'
#' @slot dea A list in which every slot is named according to a discrete feature for which differential gene expression
#' analysis has been conducted (via \code{findDeGenes()}). Every slot contains a data.frame (output of \code{Seurat::FindAllMarkers()}).
#' @slot dim_red See documentation for S4-object 'dim_red'
#' @slot fdata A data.frame containing the additionally computed features. Must contain the variables:
#' \describe{
#' \item{\emph{barcodes}}{Character. The barcode-sequences (+ the sample belonging) of every barcode spot.}
#' \item{\emph{sample}}{Character. The sample belonging of every barcode-spot.}
#' }
#'
#' @slot image A list of images named according to the samples the object contains.
#' @slot samples Character value. Contains the sample names.
#' @slot scvelo Currently not in use.
#' @slot trajectories A list named according to the samples the object contains. Each slot in
#' that list contains another list of all 'spatial_trajectory'-objects created for that sample.
#'
#' @slot used_genesets A data.frame containing the defined gene-sets. Must contain the variables:
#'
#' \describe{
#' \item{\emph{ont}}{Character. The gene-set name.}
#' \item{\emph{gene}}{Character. The belonging genes.}
#' }
#'
#' @slot version A list of four slots denoting the version of SPATA under which the object has been
#' created.
#'
#' @slot compatibility A list of miscellaneous information that mainly ensures compatibility between different
#' platforms.
#'
#' @return S4 object
#' @export
spata2 <- setClass("spata2",
slots = c(autoencoder = "list",
cnv = "list",
compatibility = "list",
coordinates ="list", #coordinates: bc, x, y, sample
data = "list",
dea = "list",
dim_red = "list", #PCA, UMAP, TSNE: bc, umap1, umap2, sample
fdata = "list", #fdata : bc, ...
gdata = "list",
images = "list",
information = "list",
samples = "character",
spatial = "list",
scvelo = "list",
trajectories = "list",
used_genesets = "data.frame",
version = "list")
)
#' @title The \code{SpatialMethod} - Class
#'
#' @description Abstracts the concept of spatial biology experiments
#' such as \emph{Visium1} or \emph{SlideSeq}.
#'
#' @slot fiducial_frame list. List of length two or three. Provides
#' standardized measures of the sample image in units of length.
#' @slot info list. List of miscellaneous meta data for the method.
#' @slot name character. The name of the spatial method. Should
#' be one of \code{validSpatialMethods()}.
#' @slot observational_unit character. Single word that describes
#' the observational unit of the experiment. E.g \emph{'barcode-spot'} in
#' case of @@name == \emph{'Visium'}.
#'
#' @export
SpatialMethod <- setClass(Class = "SpatialMethod",
slots = list(
fiducial_frame = "list",
info = "list",
name = "character",
unit = "character",
observational_unit = "character"
))
#' @title The `SpatialSegmentation` - Class
#'
#' @description Abstracts the concept of manual segmentation/annotation
#' of the sample surface.
#'
#' @slot id character. String to identify the object in a list of multiple objects of
#' the same class.
#'
#' @slot info list. Stores meta data and miscellaneous information regarding the
#' spatial segmentation. Slots that should always exist:
#' \itemize{
#' \item{sample:}{ Character string. The name of the sample (slot @@sample of the `SPATA2` object.)}
#' }
#'
#' @slot segments list. A named, nested list. Named according to the labels
#' given to each segment. E.g. list of length two with slot *necrosis* and *vivid*.
#' Each named slot is a unnamed list. In this list each slot is a list of data.frames with
#' a *x* and a *y* variable. First data.frame, named *exterior* corresponds to the exterior border of
#' the segment. Every following data.frame is named *interior*-suffix where the suffix is a number
#' and corresponds to interior holes of the segment.
#'
#' @keywords internal
#'
SpatialSegmentation <- setClass(Class = "SpatialSegmentation",
slots = list(
id = "character",
info = "list",
segments = "list"
))
#' @title The `SpatialSegment` - Class
#'
#' @description Abstracts the concept of an annotated segment within a spatial
#' segmentation.
#'
#' @slot info list. Stores meta data and miscellaneous information regarding the
#' spatial segment. Slots that should always exist:
#' \itemize{
#' \item{image_origin:}{ Character string. Content of slot @@info$origin of the `HistologyImaging` at the
#' time the segment was drawn.}
#' \item{parent_id:}{ Character string. The ID of the spatial segmentation this segment is part of.}
#' \item{pot:}{ POSIXct. The point of time when the segment was drawn. Used to handle overlapping
#' segments.}
#' \item{sample:}{ Character string. The name of the sample (slot @@sample of the `SPATA2` object.)}
#' }
#' @slot label character. Character string. The label that was given to the segment.
#' Corresponds to the group name of the barcode-spots that fall into the segment.
#' @slot polygons list. List of data.frames with *x* and *y* variables that contain
#' the vertices of the polygon. The first polygon (should be named *outer*) defines
#' the outer ring of the segment. Further polygons (should be named *inner* suffixed
#' with a number) define holes within the segment.
#'
#' @keywords internal
SpatialSegment <- setClass(Class = "SpatialSegment",
slots = list(
info = "list",
label = "character",
polygons = "list"
))
#' @title The \code{SpatialTrajectory} - Class
#'
#' @description Extension of the \code{Trajectory} for trajectories
#' that have been drawn on a surface plot.
#'
#' @slot comment character. A comment about why the trajectory was drawn.
#' @slot coords data.frame. The coordinates data.frame of the sample.
#' @slot id character. ID that uniquely identfies the trajectory in a sample.
#' @slot info list. Stores meta data and miscellaneous information regarding the
#' image annotation. Slots that should always exist:
#' \itemize{
#' \item{current_dim:}{ Numeric vector of length two. Width and height of the image
#' the @@area data.frame is currently scaled to. Used to scale the @@area data.frame
#' if the image annotation is extracted and added to a `SPATA2` object with different image resolution.}
#' \item{current_just:}{ List of two slots that track justification changes. Is used to readjust the
#' @@area data.frame if the image annotation is extracted and added to a `SPATA2` object with
#' different justifications.
#' \itemize{
#' \item{*angle*:}{ Numeric value that ranges from 0-359.}
#' \item{*flipped*:}{ List of two logical values named *horizontal* and *vertical*.}
#' }}
#' }
#' @slot projection data.frame. Data.frame that contains the length of the
#' projection of each barcode spot onto the trajectory.
#' @slot sample character. The sample name.
#' @slot segment data.frame. Contains the course of the trajetory in
#' form of a data.frame with the variables \emph{x, y, xend} and \emph{yend.}
#' @slot width numeric. The width of the rectangle that was spanned along
#' the trajectory. (Length of the rectangle corresponds to the length of
#' the segment.)
#' @slot with_unit character. The unit in which the width was specified.
#' @export
SpatialTrajectory <- setClass(Class = "SpatialTrajectory",
slots = list(
coords = "data.frame",
info = "list",
width_unit = "character"
),
contains = "Trajectory")
#' @title The \code{SpatialTrajectoryScreening} - class
#'
#' @description S4 class that contains input for and output of the
#' function \code{spatialTrajectoryScreening()}.
#'
#' @slot binwidth numeric. The width of the bins in which the barcode-spots
#' are put based on the projection length values.
#' @slot coords data.frame. Coordinates data.frame of the sample.
#' @slot id character. The ID of the screened trajectory.
#' @slot method_padj character. The method with which p-values were adjusted.
#' @slot models data.frame. The model data.frame that has been used for the
#' screening.
#' @slot n_bins numeric. The number of bins in which the barcode-spots
#' are distributed based on their projection length.
#' @slot results data.frame. A data.frame that contains the model evaluations
#' @slot sample character. The sample name.
#' @slot summarize_with character. The name of the function that has been
#' used to summarize the variables by bin.
#' @slot spatial_trajectory SpatialTrajectory. The spatial trajectory based on
#' which the screening took place.
#'
#' @export
#'
SpatialTrajectoryScreening <- setClass(Class = "SpatialTrajectoryScreening",
slots = list(
binwidth = "numeric",
coords = "data.frame",
id = "character",
method_padj = "character",
models = "data.frame",
n_bins = "numeric",
results = "data.frame",
sample = "character",
summarize_with = "character",
spatial_trajectory = "SpatialTrajectory"
))
# T -----------------------------------------------------------------------
# Trajectory - other S4 classes inherit from it. Is listed on top under 0
#' @title The \code{Visium} - Class
#'
#' @description Abstracts the concept of 10X Visium spatial biology experiments.
#'
#' @slot capture_area list. List of length two. Provides
#' standardized measures of the active region where tissue can
#' be placed on a Visium slide.
#' @slot ccd character. The center to center distance
#' of the barcoded spots provided in a valid `SPATA2` spatial measure.
#' @slot fiducial_frame list. List of length two. Provides
#' standardized measures of spots help the sample microscopist see where
#' to place tissue and are also used by Space Ranger to determine
#' where the capture area is in an image.
#' @slot info list. List of miscellaneous meta data for the method.
#' @slot name character. The name of the spatial method.
#' @slot observational_unit character. Single word that describes
#' the observational unit of the experiment.
#'
#' @inheritSection section_dummy Distance measures
#'
#' @export
Visium <- setClass(Class = "Visium",
contains = "SpatialMethod",
slots = list(
capture_area = "list",
ccd = "character",
fiducial_frame = "list"
)
)
# Deprecated --------------------------------------------------------------
#' data_counts object
#'
#' @slot counts A sparse matrix containing the original counts.
#' @slot norm_exp A processed expression matrix. Rownames must be the gene-names.
#' Column names must be the barcodes.
#'
#' @return S4 object
#' @export
#' @keywords internal
data_counts <- setClass("data_counts",
slots = c(counts = "Matrix",
norm_exp = "matrix"))
#' dim_red object
#'
#' @slot UMAP A data.frame containing the variables \emph{'barcdoes', 'sample', 'umap1', 'umap2'}
#' @slot TSNE A data.frame containing the variables \emph{'barcodes', 'smaple', 'tsne1', 'tsne2'}
#'
#' @return S4 object
#' @export
#' @keywords internal
dim_red <- setClass("dim_red",
slots = c(UMAP = "data.frame",
TSNE ="data.frame"))
#' @title The \code{HistologyImage} - Class
#'
#' @description S4 class that represents histology images.
#'
#' @slot annotations list. List of objects of class \code{ImageAnnotation}.
#' @slot dir_default character. The default directory that is used to load
#' the image if slot @@image is empty. Or a string linking to the default slot
#' ('highres' or 'lowres').
#' @slot dir_highres character. Directory to the high resolution version of the image.
#' @slot dir_lowres character. Directory to the low resolution version of the image.
#' @slot grid data.frame. A data.frame that contains at least a variable
#' named \emph{x} and a variable named \emph{y} representing a grid.
#' @slot id character. String to identify the object in a list of multiple objects
#' of the same class. Usually refers to the sample name of the \code{SPATA2} object.
#' @slot image Image.
#' @slot info list. A flexible list that is supposed to store miscellaneous
#' information around the image.
#' @slot misc list. A flexible list for miscellaneous input.
#' @keywords internal
#' @export
HistologyImage <- setClass(Class = "HistologyImage",
slots = list(
annotations = "list",
coordinates = "data.frame",
dir_default = "character",
dir_highres = "character",
dir_lowres = "character",
grid = "list",
id = "character",
info = "list",
image = image_class,
misc = "list"
))
#' spatial_trajectory object
#'
#' @slot compiled_trajectory_df A data.frame containing the variables:
#'
#' \describe{
#' \item{\emph{barcodes}}{Character. The barcode-spots' sequences.}
#' \item{\emph{sample}}{Character. The barcode-spots' sample belonging.}
#' \item{\emph{x,y}}{Numeric. The barcode-spots' spatial coordinates.}
#' \item{\emph{projection_length}}{Numeric. The distance between the barcode-spots'
#' projection onto the trajectory-vector and the start of the trajectory.}
#' \item{\emph{trajectory_part}}{Character. The part of the trajectory.}
#' }
#'
#'
#' @slot segment_trajectory_df A data.frame containing the numeric variables
#' \emph{x, y, xend, yend} that denote the start and the end of every trajectory
#' part.
#' @slot comment Character value. The comment written down before saving the trajectory.
#' @slot name Character value. The trajectory's name.
#' @slot sample Character value. The sample the trajectory belongs to.
#'
#' @return S4 object
#' @export
#' @keywords internal
spatial_trajectory <- setClass("spatial_trajectory",
slots = c(
compiled_trajectory_df = "data.frame",
segment_trajectory_df = "data.frame",
comment = "character",
name = "character",
sample = "character"))
#' default instructions
#' @export
#' @keywords internal
default_instructions <- setClass(Class = "default_instructions",
slots = c(
average_genes = "logical",
binwidth = "numeric",
clrp = "character",
clrsp = "character",
colors = "character",
complete = "logical",
concavity = "numeric",
display_facets = "logical",
display_image = "logical",
display_labels = "logical",
display_legend = "logical",
display_points = "logical",
display_residuals = "logical",
display_trajectory_parts = "logical",
display_title = "logical",
expand_outline = "numeric",
max_adj_pval = "numeric",
method_aggl = "character",
method_dist = "character",
method_de = "character",
method_dr = "character",
method_hclust = "character",
method_ovl = "character",
method_padj = "character",
method_gs = "character",
min_lfc = "numeric",
n_highest_lfc = "numeric",
n_lowest_pval = "numeric",
n_pcs = "numeric",
normalize = "logical",
position = "character",
pt_alpha = "numeric",
pt_clr = "character",
pt_clrp = "character",
pt_clrsp = "character",
pt_fill = "character",
pt_shape = "numeric",
pt_size = "numeric",
pt_size_fixed = "logical",
relevel = "logical",
scales = "character",
sgmt_clr = "character",
sgmt_size = "numeric",
show_colnames = "logical",
show_rownames = "logical",
smooth = "logical",
smooth_clr = "character",
smooth_method = "character",
smooth_se = "logical",
smooth_span = "numeric",
uniform_genes = "character",
verbose = "logical")
)
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