[FEAT] - quick fix for ggridges

R/utils_global.R

@@ -390,9 +390,7 @@ normalisation_qfeatures <- function(qfeatures, method) {
 #' 
 #' @rdname INTERNAL_density_by_sample_plotly
 #' @keywords internal
-#' @importFrom plotly ggplotly
-#' @importFrom ggplot2 ggplot aes
-#' @importFrom ggridges geom_density_ridges
+#' @importFrom SummarizedExperiment assay colData
 
 density_by_sample_plotly <- function(qfeatures, color) {
 
@@ -407,11 +405,149 @@ density_by_sample_plotly <- function(qfeatures, color) {
 
         combined_df <- rbind(combined_df, assay_df)
     }
-    print(colData(qfeatures)[combined_df$sample, color])
+
     combined_df$color <- colData(qfeatures)[combined_df$sample, color]
 
-    plot <- ggplot(combined_df, aes(x = intensity, y = sample, fill = color)) +
-        geom_density_ridges()
-
-    ggplotly(plot)
-}
+    plotlyridges(
+        data = combined_df,
+        vardens = "intensity",
+        varcat = "sample")
+}
+
+# This function comes from the github repo rushkin/bitsandends 
+# Thanks to iliarushkin for this function
+
+#' Mimicks \code{ggridges} but using \code{plotly} so that the output is interactive
+#'
+#' @param data data-frame of data to plot
+#' @param vardens name of the column in \code{data} to use on the x-axis ('density variable')
+#' @param varcat name of the column in \code{data} to use for splitting plots ('category variable')
+#' @param linecolor line color
+#' @param fillcolor fill color
+#' @param fillopacity fill opacity
+#' @param linewidth line width
+#' @param scale vertical scale of plots, compared to the spacing between plots.
+#' @param logspaced boolean, whether to use log-spaced points in calculating density
+#' @param cut.from how much to cut into the region to the left of the smallest data values, in units of the bandwidth.
+#' @param cut.to how much to cut into the region to the right of the greatest data values, in units of the bandwidth.
+#' @param n number of points used in calculation of density
+#' @param bw bandwidth to use in density calculation. if NULL, uses the default of \code{density}.
+#' @param bw.separate if TRUE, will use separately estimated bandwidth in each plot, overriding \code{bw}
+#' @param height.norm vertical normalization of plots. If 'integral', will normalize to unit area under the curve. If '1' will normalize to unit maximum height
+#' @param round.digits number of rounding digits used in hover labels
+#' @param x.min lower end of the x-axis range
+#' @param height passed as \code{height} to the plotly object
+#' @param width passed as \code{width} to the plotly object
+#' @return a plotly object
+#' 
+#' @rdname INTERNAL_plotlyridges
+#' @keywords internal
+#' @importFrom plotly plot_ly add_trace layout
+#' 
+plotlyridges=function(data,vardens,varcat,linecolor='darkblue',fillcolor='steelblue',fillopacity=0.6,linewidth=0.5,scale=0.9,logspaced=FALSE,cut.from=0, cut.to=3,n=512,bw=NULL,bw.separate=FALSE,height.norm='integral',round.digits=2,x.min=0
+                      ,height=NULL
+                      ,width=NULL
+){
+
+  data=subset(data,!is.na(data[,vardens]))
+
+  r=range(data[,vardens])
+
+  if(is.null(bw)){
+    if(!bw.separate){
+      if(logspaced){
+        x=log(data[,vardens])
+      }else{
+        x=data[,vardens]
+      }
+      if(length(x)>1){
+        bw=density(x)$bw
+      }else{
+        bw=1
+      }
+    }
+  }
+
+  df=aggregate(data[,vardens],by=list(varcat=data[,varcat]),FUN=function(x){
+
+    if(length(x)==0) return(NULL)
+    if(bw.separate){
+      if(length(x)==1){
+        bw=1
+      }else{
+        bw='nrd0'
+      }
+    }
+    if(logspaced){
+      x=log(x)
+    }
+    from=min(x,na.rm=TRUE)-cut.from*bw
+    to=max(x,na.rm=TRUE)+cut.to*bw
+    d=density(x,bw=bw,n=n,from=from,to=to)[1:2]
+    #Normalize height
+    if(height.norm=='1'){
+      d$y=d$y/max(d$y)
+    }
+    if(height.norm=='integral'){
+      d$y=d$y/(sum(d$y)*(d$x[2]-d$x[1]))
+    }
+
+    if(logspaced){
+      d$x=exp(d$x)
+      d$y=d$y/d$x
+    }
+
+
+    return(d)
+  })
+
+  text=aggregate(data[,vardens],by=list(varcat=data[,varcat]),FUN=function(x){
+
+    x=x[!is.na(x)]
+    q=quantile(x)
+    text=paste0('Observations: ',prettyNum(length(x),big.mark=','),'<br>Median: ',round(q[3],round.digits),'<br>Range: [',round(q[1],round.digits),', ',round(q[5],round.digits),']','<br>Interquartile Range: [',round(q[2],round.digits),', ',round(q[4],round.digits),']')
+    return(text)
+  })$x
+
+
+
+
+  catnames=df[[1]]
+  x=df[[2]][1:(length(df[[1]]))]
+  y=df[[2]][-(1:(length(df[[1]])))]
+
+
+
+  ymax=max(unlist(y),na.rm=TRUE)
+  y=lapply(y,function(yy){
+    yy=scale*yy/ymax
+    return(yy)
+  })
+  p=plotly::plot_ly(type='scatter',mode='lines',height=height,width=width)
+
+  fillcolor=as.vector(col2rgb(fillcolor))/255
+  fillcolor=rgb(fillcolor[1],fillcolor[2],fillcolor[3],alpha=fillopacity)
+
+
+  if(is.null(x.min)){
+    xaxis=list(range=r)
+  }else{
+    xaxis=list(range=c(x.min,r[2]))
+  }
+
+  for(i in rev(1:length(catnames))){
+
+    p=plotly::add_trace(p,x=x[[i]],y=i, line=list(color=linecolor,width=linewidth),showlegend=FALSE,hoverinfo='none')
+    p=plotly::add_trace(p,
+      x=x[[i]],y=y[[i]]+i,fill='tonexty', fillcolor=fillcolor, line=list(color=linecolor,width=linewidth),showlegend=FALSE, name=catnames[i],hoverinfo='text',text=text[i]
+    )
+
+    p=plotly::layout(p,
+      yaxis=list(tickmode='array',tickvals=(1:length(catnames)),ticktext=catnames,showline=TRUE)
+      ,xaxis=xaxis
+    )
+
+  }
+  p
+  return(p)
+}