argument_dummy: Argument dummy

In kueckelj/SPATA2: A Toolbox for Spatial Gene Expression Analysis

Argument dummy

Description

Argument dummy

Usage

argument_dummy(
  clrp,
  clrsp,
  display_points,
  display_facets,
  scales,
  ncol,
  nrow,
  verbose
)

Arguments

clrp	Character value. Specifies the color palette to be used to represent groups of discrete variables. Run validColorPalettes() to obtain valid input options.
clrsp	Character value. Specifies the color spectrum to be used to represent continuous values of numeric variables. Run validColorSpectra() to obtain valid input options.
display_points	Logical value. If set to TRUE points are used additionally to display the results.
display_facets	Logical value. If set to TRUE the plot is split via ggplot2::facet_wrap() such that each variable gets it's own subplot.
scales, ncol, nrow	Affects the way the subplots are displayed.
nrow, ncol	Numeric values or NULL. Used to arrange multiple plots.
verbose	Logical. If set to TRUE informative messages regarding the computational progress will be printed. (Warning messages will always be printed.)
across	Character value or NULL. Specifies the grouping variable of interest. Use getGroupingOptions() to obtain all variable names that group the barcode spots of your object in a certain manner.
across_subset	Character vector or NULL. Specifies the particular groups of interest the grouping variable specified in argument across contains. If set to NULL all of them are chosen. You can prefix groups you are NOT interested in with a '-'. (Saves writing if there are more groups you are interested in than groups you are not interested in.) Use getGroupNames() to obtain all valid input options.
bcsp_rm	Character vector or NULL. If character, specifies barcode-spots that are removed before analysis or plotting.
clrp_adjust	Named character vector or NULL. If character, it adjusts the color palette that is used to represent the groups. Names of the input vector must refer to the group and the respective named element denotes the color with which to represent the group.
concavity	Given to concavity of ggforce::geom_mark_hull(). Can be optimized for every sample via object <- setDefault(object, concavity = ...). Default by object initiation is 1.
dir	Character value. The chosen directory. See details for possible requirements.
discrete_feature	Character value. Specifies the name of the grouping variable of interest. Use getGroupingOptions() to obtain all valid input options.
display_ribbon	Logical value. If TRUE, a ribbon is displayed around the main line of the plot visualizing uncertainty using standard deviation.
display_title	Logical value. If set to TRUE an informative title is displayed.
error	Logical. If TRUE and the input is invalid the function throws an error.
expand_x, expand_y	Given to argument expand of ggplot2:scale_x/y_continuous().
expand	Specifies image expansion. An image that is cropped based on an image annotation centers around the image annotation. If expand = 0, the default, the dimensions of the image, that is width/x-axis and height/y-axis, are set to include only the image annotation area and nothing more. Using expand, the cropped image section can be adjusted. See section Expansion of cropped image sections for more information.
expand_outline	Distance measure by which the outline of the area is expanded.
ggpLayers	List of ggproto-objects that are added to each plot. Skim ggpLayer*()-functions for more options.
grouping_variable	Character value. The grouping variable of interest. Use getGroupingOptions() to obtain all valid input options.
h	Numeric value or vector or NULL (see details for more). Denotes the height at which the dendrogom is cut.
hline_alpha, hline_color, hline_size, hline_type	Parameters given to ggplot2::geom_hline() that control the appearance of vertical lines of the plot.
ids	Character vector or NULL. If character, specifies the IDs of the image annotations of interest. If numeric, the image annotations are picked by number. If NULL, all image annotations are included - subsequent selection with tags and test is possible.
inner	Logical value. Only applies if an image annotation contains a secondary image annotation within its own area. If FALSE, the inner borders of the image annotation are not included in the output.
k	Numeric value or vector or NULL (see details for more). Denotes the number of clusters in which the hierarchical tree is supposed to be split.
method_de	Character value. Denotes the method to according to which the de-analysis is performed. Given to argument test.use of the Seurat::FindAllMarkers()-function. Run SPATA::dea_methods to obtain all valid input options.
method_gs	Character value. The method according to which gene sets will be handled specified as a character of length one. This can be either 'mean or one of 'gsva', 'ssgsea', 'zscore', or 'plage'. The latter four will be given to gsva::GSVA().
method_padj	Character value. The method with which adjusted p-values are calculated. Use validPadjMethods() to obtain all valid input options.
n_bcsp	Numeric value. Specifies the sample size of barcode-spots and can be set to prevent overplotting.
n_bins	Numeric value. Specifies the exact number of bins the barcodes are binned into.
n_gsets	Numeric value. Maximal number of gene sets whose results are included. The first n_gsets are included starting with the one with the lowest significance value.
normalize	Logical. If set to TRUE values will be scaled to 0-1. Hint: Variables that are uniformly expressed can not be scaled and are discarded.
line_alpha	Numeric. Affects alpha of main lines of the plot.
line_color	Character. Affects color of the main lines of the plot.
line_size	Numeric. Affects size of the main lines of the plot.
line_type	Character. The line type. One of 'blank', 'solid', 'dashed', 'dotted', 'dotdash', 'longdash' and 'twodash'.
linesize	Numeric value. The size of the line(s) plotted.
object	An object of class spata2.
order	Logical value. If TRUE, data points are ordered according to their values before beeing plotted.
order_by	Character value or NULL. If character, the specified variable is used to order the data points.
order_desc	Logical value. If TRUE, reverses the arrangement specified via order_by and/or order.
outer	Logical value. Only applies if an image annotation contains a secondary image annotation within its own area. If FALSE, the outer border of the image annotation is not included in the output.
overwrite	Logical value. Must be TRUE to allow overwriting.
pt_alpha	Numeric value. Specifies the degree of transparency of all points.
pt_clr	Character value. Specifies the color of all points.
pt_clrp	The color palette to be used if the specified variable displayed by color is categorical/discrete. Run validColorPalettes() to see valid input.
pt_clrsp	The color spectrum to be used if the specified variable displayed by color is continuous. Run validColorSpectra() to see valid input.
pt_size	Numeric value. Specifies the size of all points.
relevel	Logical value. If set to TRUE the input order of across_subset determines the order in which the groups of interest are displayed. Groups that are not included are dropped which affects the colors with which they are displayed.
sc_input	Data.frame that contains the results from single cell deconvolution. Must have at least three columns: x : numeric. Position of cell on the x axis in pixel., y : numeric. Position of cell on the y axis in pixel., cell_type : factor Cell type of the cell.
sctm_interpolate, sctm_pixels	Given to the corresponding arguments of scattermore::geom_scattermore(). Note: With increasing sctm_pixels the point size must be adjusted with the argument pt_size.
sgmt_alpha, sgmt_color, sgmt_size, sgmt_type	Parameters given to ggplot2::geom_segment() that control the appearance of segments of the plot.
signif_var	Character value. Determines what to be considered while checking for significance. Either 'pval' (p-Value) or 'fdr' (False Discovery Rate).
signif_threshold	Numeric value. Significance values below signif_threshold are not included.
simplify	Logical. If set to TRUE the output list is simplified to a vector if possible. If set to FALSE a list is returned.
smooth	Logical. If TRUE, a loess fit is used to smooth the values.
smooth_span	Numeric value. Controls the degree of smoothing. Given to argument span of stats::loess().
square	Logical value. Most image annotations come in variable shapes and have different horizontal and vertical diameters. Therefore, height and width of the image section are usually not equal. If square = TRUE, the cropped section of the image that contains the annotated structure is forced into a square: the bigger diameter of both is taken as default. E.g. if the horizontal diameter of the image annotation is 1mm and the vertical diameter is 1.5mm, the output image will have height and width of 1.5mm. That is, in terms of coordinates, an x-range and a y-range of 1.5mm. Processing of the image output depending on argument expand happens afterwards.
summarize_with	Character value. Name of the function with which to summarize.
spatial_method	Character value. The name of the spatial method that underlies the experiment. Must be one of validSpatialMethods(). Defaults to 'Unknown'.
tags	Character vector or NULL. If character, the tags for the image annotation selection. See section Selection of image annotation with tags for more information.
test	Character value. One of any. all, identical, not_identical and none. Specifies how input for tags is used to select image annotations. See section Selection of image annotation with tags for more information.
text_alpha, text_color, text_nudge_x, text_nudge_y, text_size, text_type	Parameters given to ggplot2::geom_text() that control the appearance of text of the plot.
transform_with	List or NULL. If list, can be used to transform continuous variables before plotting. Names of the list slots refer to the variable. The content of the slot refers to the transforming functions. Slot content can either be a character vector of function names. Use validScaleTransformations() to obtain all valid character value inputs. Or it can be a list of functions (and function names). Useful if you want to apply more than one transformation on variables mapped to plotting aesthetics. Input for transform_with is applied before the respective <aes>_trans argument.
use_scattermore	Logical value. If TRUE, data points are plotted with scattermore::geom_scattermore() which allows quick plotting of several thousand data points. If the number of data points plotted is bigger than 10.000 it is used anyway.
vline_alpha, vline_color, vline_size, vline_type	Parameters given to ggplot2::geom_vline() that control the appearance of vertical lines of the plot.
whole_sample	Logical. If TRUE, normalization of the values used takes place in the light of the complete sample.
x_nth	Numeric value. If the number of breaks/labels on the x-axis becomes too high x_nth can be used to reduce it. If x_nth is 1, every label is kept. If 2, every second label is kept. If 3, every third label is kept. And so on.
xrange, yrange	Vector of length two or NULL. If not NULL, specifies the x- and y-range to which the output image is cropped. E.g. xrange = c(200, 500) results in the image being cropped from x-coordinate 200px up to x-coordinate 500px. If NULL, the original image ranges are taken. This argument works within the SPATA2 distance framework. If values are specified in European units of length the input is immediately converted to pixel units. See info section Distance measures for more information.
...	Used to absorb deprecated arguments or functions.

kueckelj/SPATA2 documentation built on March 16, 2024, 10:25 a.m.