plotMatrix raster grobs change to rectangle grobs

DESCRIPTION

@@ -60,7 +60,9 @@ Imports:
     utils,
     grDevices,
     graphics,
-    grid
+    grid,
+    tibble,
+    tidyr
 biocViews:
     FunctionalGenomics,
     Visualization,

NAMESPACE

@@ -233,10 +233,12 @@ importFrom(graphics,segments)
 importFrom(graphics,text)
 importFrom(grid,addGrob)
 importFrom(grid,gTree)
+importFrom(grid,gpar)
 importFrom(grid,grid.draw)
 importFrom(grid,grid.ls)
 importFrom(grid,grid.newpage)
 importFrom(grid,rasterGrob)
+importFrom(grid,rectGrob)
 importFrom(grid,unit)
 importFrom(grid,viewport)
 importFrom(magrittr,`%<>%`)
@@ -264,6 +266,9 @@ importFrom(strawr,readHicBpResolutions)
 importFrom(strawr,readHicChroms)
 importFrom(strawr,readHicNormTypes)
 importFrom(strawr,straw)
+importFrom(tibble,as_tibble)
+importFrom(tibble,rownames_to_column)
+importFrom(tidyr,pivot_longer)
 importFrom(utils,capture.output)
 importFrom(utils,tail)
 importMethodsFrom(IRanges,countOverlaps)

R/methods-plotMatrix.R

@@ -140,9 +140,11 @@
 #' @importFrom RColorBrewer brewer.pal
 #' @importFrom plotgardener mapColors
 #' @importFrom grid viewport unit grid.newpage gTree grid.ls rasterGrob
-#'  addGrob grid.draw
+#'  addGrob grid.draw rectGrob gpar
 #' @importFrom rlang inform
 #' @importFrom grDevices colorRampPalette
+#' @importFrom tibble as_tibble rownames_to_column
+#' @importFrom tidyr pivot_longer
 #' @noRd
 .plotMatrix <- function(data, params, x, y, width, height,
                         just, default.units, draw, palette, zrange,
@@ -207,15 +209,20 @@
     m <- matrix(data=colv,
                 nrow=nrow(matrixPlot$data),
                 ncol=ncol(matrixPlot$data))
+
+    ## Convert matrix to tibble where column names = col number and add rownum
+    colnames(m) <- seq(1, ncol(m))
+    m_tibble <- as_tibble(m)
+    m_tibble <- rownames_to_column(m_tibble, var = "rownum")
+
+    ## Convert to 3-column df with rownum, colnum, and color columns
+    m_long <- pivot_longer(m_tibble, 
+                           !rownum, 
+                           names_to = "colnum", 
+                           values_to = "color")
 
     ## Viewports ---------------------------
 
-    ## Get viewport name
-    currentViewports <- plotgardener:::current_viewports()
-    nVp <- length(grep("MatrixPlot", currentViewports))
-    vp_name <- paste0("MatrixPlot", nVp + 1)
-
-
     ## If placing information is provided but plot == TRUE,
     ## set up it's own viewport separate from pageCreate
 
@@ -227,15 +234,21 @@
                        height=unit(1, "snpc"),
                        width=unit(1, "snpc"),
                        clip="on",
+                       xscale = c(0, ncol(matrixPlot$data)),
+                       yscale = c(nrow(matrixPlot$data), 0),
                        just="center",
-                       name=vp_name)
+                       name="MatrixPlot1")
 
         if (matrixPlot$draw){
-            vp$name <- "MatrixPlot1"
             grid.newpage()
         }
 
     } else {
+
+        ## Get viewport name
+        currentViewports <- plotgardener:::current_viewports()
+        nVp <- length(grep("MatrixPlot", currentViewports))
+        vp_name <- paste0("MatrixPlot", nVp + 1)
 
         ## Check that plotgardener page exists
         plotgardener:::check_page(
@@ -252,6 +265,8 @@
                        height=page_coords$height,
                        width=page_coords$width,
                        clip="on",
+                       xscale = c(0, ncol(matrixPlot$data)),
+                       yscale = c(nrow(matrixPlot$data), 0),
                        just=matrixPlot$just,
                        name=vp_name)
     }
@@ -271,13 +286,20 @@
     name <- paste0("MatrixPlot", nObjs + 1)
 
     ## Make grobs
-    mpRaster <- rasterGrob(image=m, interpolate=FALSE, name=name)
+    mpSquares <- rectGrob(x = m_long$colnum,
+                          y = m_long$rownum,
+                          just = c("right", "top"),
+                          width = 1,
+                          height = 1,
+                          gp = gpar(col = NA, fill = m_long$color),
+                          default.units = "native",
+                          name = name)
 
     ## Assign grobs to gTree
     assign(x="MatrixPlotGrobs",
            value=addGrob(gTree=get(x="MatrixPlotGrobs",
                                    envir=plotgardener:::pgEnv),
-                         child=mpRaster),
+                         child=mpSquares),
            envir=plotgardener:::pgEnv)
 
     ## Add grobs to object
@@ -289,7 +311,7 @@
     }
 
     ## Return object --------------------------
-    inform(paste0("MatrixPlot[", mpRaster$name, "]"))
+    inform(paste0("MatrixPlot[", mpSquares$name, "]"))
     invisible(matrixPlot)
 }