joinWith: Join barcodes with additional variables
In kueckelj/SPATA2: A Toolbox for Spatial Gene Expression Analysis

joinWith

R Documentation

Join barcodes with additional variables

Description

Each member of the joinWith()-family takes a data.frame as input that contains at least the variables barcodes and sample. (Easily obtained with the get*()-family.) It extracts the specified variables and joins them over the barcode variable with the provided data.frame.

Usage

joinWith(
  object,
  spata_df = getCoordsDf(object),
  features = NULL,
  gene_sets = NULL,
  method_gs = NULL,
  genes = NULL,
  average_genes = NULL,
  uniform_genes = NULL,
  smooth = FALSE,
  smooth_span = NULL,
  verbose = NULL,
  normalize = NULL
)

joinWithFeatures(
  object,
  spata_df = getCoordsDf(object),
  features,
  smooth = FALSE,
  smooth_span = 0.02,
  verbose = TRUE
)

joinWithGenes(
  object,
  spata_df = getCoordsDf(object),
  genes,
  average_genes = FALSE,
  uniform_genes = "keep",
  smooth = FALSE,
  smooth_span = 0.02,
  normalize = TRUE,
  verbose = TRUE
)

joinWithGeneSets(
  object,
  spata_df = getCoordsDf(object),
  gene_sets,
  method_gs = "mean",
  smooth = FALSE,
  smooth_span = 0.02,
  normalize = TRUE,
  verbose = TRUE,
  ignore = T
)

joinWithVariables(
  object,
  spata_df = getCoordsDf(object),
  variables,
  method_gs = "mean",
  average_genes = FALSE,
  uniform_genes = "discard",
  smooth = FALSE,
  smooth_span = 0.02,
  normalize = TRUE,
  verbose = TRUE
)

Arguments

`object`	An object of class `spata2`.
`features`	The features of interest specified as a character vector.
`gene_sets`	The gene sets of interest specified as a character vector.
`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().
`genes`	The genes of interest specified as a character vector.
`average_genes`	Logical. If set to TRUE the average expression of the specified genes is calculated and saved under one variable named 'mean_genes'.
`uniform_genes`	Character value. If set to 'discard' genes that are uniformly expressed across all barcode-spots of the specified coordinates data.frame are discarded. If set to 'keep' they are kept.
`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()`.
`verbose`	Logical. If set to TRUE informative messages regarding the computational progress will be printed. (Warning messages will always be printed.)
`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.
`variables`	Character vector. The variables of interest: Gene sets: Must be in `getGeneSets()` Genes: Must be in `getGenes()` Features: Must be numeric ones of `getFeatureNames()`