R/0.1_MolDiaISS_class.R

In mashranga/MolDia: Single cell In-Situ sequencing (ISS) data analysis

#' The ISS data class for segmentated file
#' 
#' @description The MolDiaISS class is a main object for all ISS based analysis. 
#'              A MolDiaISS class object has the following slot
#'
#' @slot data Main data for analysis
#' @slot norm.data Normalized data (log-scale).
#' @slot scale.data Scaled (default is z-scoring each gene) expression matrix; used for dimmensional reduction and heatmap visualization.
#' @slot location Insitu location of RCA cell location on X and Y co-ordinate.
#' @slot gene Name of genes in the data.
#' @slot cluster Cluster identification of all cells
#' @slot cluster.marker Marker gene of each cluster.
#' @slot tsne.data tSNE co-ordinate for data.
#' @slot pca.data List of stored dimmensional reductions
#'
#' @section Dataclass: Data class section
#'
#' @name MolDiaISS
MolDiaISS <- methods::setClass(Class = "MolDiaISS",
                               slots = c(data           = "data.frame",
                                         norm.data      = "matrix",
                                         scale.data     = "matrix",
                                         gene           = "vector",
                                         cluster        = "factor",
                                         location       = "data.frame",
                                         cluster.marker = "list",
                                         tsne.data      = "data.frame",
                                         pca.data       = "list"))


methods::setMethod( f = "show", signature = "MolDiaISS",
                    definition = function(object)
                      {
                      cat( "An object of class", class(object),
                           "\nNumber of genes:", ncol(object@data),#sum(colSums(object@data)>=0),
                           "\nNumber of cells:", nrow(object@data),#sum(rowSums(object@data)>=0),
                           "\nNumber of reads:", sum(object@data),
                           if(length(object@cluster) > 0) "\nCluster id:", levels(object@cluster),
                           if(length(object@cluster) > 0) "\nCluster size:",table(object@cluster))
                      invisible(x = NULL)
                      }
                    )
MolDiaISS <- methods::new("MolDiaISS")


#' The ISS data class for non-segmentated file
#' @description  The MolDiaISS_nonsegment class is the non segmentated data class.
#' 
#' @slot reads Reads name of the data.
#' @slot gene Name of genes in the data.
#' @slot tile ParentCell and tile of the data.
#' @slot quality Quality information of the data.
#' @slot location In-situ location of the gene in the data
#' 
#' @name MolDiaISS_nonsegment
MolDiaISS_nonsegment <- methods::setClass(Class = "MolDiaISS_nonsegment",
                                          slots = c(reads     = "data.frame",
                                                    gene      = "vector",
                                                    tile      = "data.frame",
                                                    quality   = "data.frame",
                                                    location  = "data.frame"))
methods::setMethod( f = "show", signature = "MolDiaISS_nonsegment",
                    definition = function(object)
                    {
                      cat( "An object of class", class(object),
                           "\nNumber of genes:", length(unique(object@gene)),
                           "\nNumber of reads:", nrow(object@reads))
                           invisible(x = NULL)
                    }
                      )
MolDiaISS_nonsegment <- methods::new("MolDiaISS_nonsegment")