R/SignatureScatterPlot.R

In nbroguiere/burgertools: Collection of tools extending the functionality of Seurat

#' Scatter plots of signature scores on single cells
#'
#' Plots various signature scores (or features) against another signature score, in an interactive plot, in order to help define gates. In the scatter plot, each point represents a cell in the Seurat object. The points can be colored either by identity or according to a feature. Generalizes FeatureScatter() in that several scatter plots can be done at once, features and signatures can be pulled from several assays as well as from the metadata simultaneously, coloring can be done according to a feature instead of Idents(), and hovering can be used to get coordinates.
#'
#' @param object Seurat object.
#' @param sign1 character(1). The name of the signature to plot on the x axis.
#' @param sign2 character(n). The name of the signature(s) to plot on the y axis.
#' @param pt.size numeric(1).The point size. Default: 0.8.
#' @param n.rows numeric(1).The number of rows in the plot grid. NA for automatic smart choice. Default: NA.
#' @param color.by character(n). The name of a metadata or feature column or a vector of idents or values to be used for point colors.
#'
#' @return A plotly grid of plots
#' @keywords Signature Scatter Plot
#' @export
#' @examples
#' SignatureNames <- names(MySignatureList)
#' SignatureScatterPlot(MySeuratObject,SignatureNames[1],SignatureNames[2])
#' SignatureScatterPlot(MySeuratObject,SignatureNames[1],SignatureNames[2:length(SignatureNames)])
#' SignatureScatterPlot(MySeuratObject,SignatureNames[1],SignatureNames[2:length(SignatureNames)],pt.size=1.2,n.rows=4)

SignatureScatterPlot <- function(object,sign1,sign2,pt.size=0.8,n.rows=NA,color.by=Idents(object)){
  if(length(sign1)>1 | !is.character(sign1[1])){
    stop("sign1 should be a character vector of length 1.")
  }
  sign2 <- unlist(sign2)
  n <- length(sign2)


  # Gather the signatures and features to plot:
  df <- GatherFeatures(object,c(sign1,sign2))

  # Add the color information to the data frame:
  if(length(color.by)==1){
    color.by_name <- color.by
    color.by <- GatherFeatures(object,color.by)[,1]
  }else{
    color.by_name <- "legend"
  }
  df <- cbind(df,color.by=color.by)
  colnames(df)[ncol(df)] <- color.by_name

  # Plot
  p <- list()
  for(i in 1:n){
    p[[i]] <- plotly::ggplotly(ggplot2::ggplot(df)+ggplot2::geom_point(aes_string(paste0("`",sign1,"`"),paste0("`",sign2[i],"`"),color=paste0("`",color.by_name,"`")),size=pt.size)+ggplot2::ylab(label = sign2[i]))
    p[[i]] <- plotly::add_annotations(p[[i]], text = paste0(sign2[i]," vs ",sign1), x = 0.5, y = 1, yref = "paper", xref = "paper", xanchor = "middle", yanchor = "top", showarrow = FALSE, font = list(size = 15))

    if(i>1){
      p[[i]] <- plotly::style(p[[i]],showlegend=FALSE) # Make sure the legend is only shown once
    }
  }

  # Decide the grid dimensions
  if(is.na(n.rows)){
    if(n<=2){
      n.rows <- 1
    }else if(n<=6){
      n.rows <- 2
    }else if(n<=12){
      n.rows <- 3
    }else if(n<=16){
      n.rows <- 4
    }else{
      n.rows <- floor(sqrt(n))
    }
  }
  return(plotly::subplot(p, nrows = n.rows))
}