add repel arg to plotIndiv and plotVar. re mixOmicsTeam#129

aljabadi · Jun 1, 2021 · efa7dba · efa7dba
1 parent f1671f8
commit efa7dba
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Showing 9 changed files with 70 additions and 7 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -28,6 +28,7 @@ Suggests: BiocStyle,
           knitr, 
           rmarkdown, 
           testthat, 
+          ggrepel, 
           rgl
 Authors@R: 
     c(person("Kim-Anh", "Le Cao", role = c("aut", "cre"), email = "[email protected]"), 

diff --git a/R/internal_graphicModule.R b/R/internal_graphicModule.R
@@ -57,6 +57,7 @@ internal_graphicModule <-
              zlim,
              class.object,
              display.names,
+             repel = FALSE,
              legend,
              abline,
              star,
@@ -258,11 +259,13 @@ internal_graphicModule <-
                 {
                     if (display.names)
                     {
-                        p = p +geom_point(data = subset(df, col == i &
-                                                            df$Block == levels(df$Block)[j]),size = 0, shape = 0,
+                        .geom_text <- .get_geom_text(repel = repel, style = style)
+
+                        p = p + geom_point(data = subset(df, col == i &
+                                                            df$Block == levels(df$Block)[j]),size = ifelse(repel, 2, 0),
                                           color = unique(df[df$col == i & df$Block ==
-                                                                levels(df$Block)[j], ]$col))+
-                            geom_text(data = subset(df, col == i & df$Block ==
+                                                                levels(df$Block)[j], ]$col), shape = 16)+
+                            .geom_text(data = subset(df, col == i & df$Block ==
                                                         levels(df$Block)[j]),
                                       aes(label = names),
                                       color = df[df$col == i & df$Block ==

diff --git a/R/plotIndiv.R b/R/plotIndiv.R
@@ -66,6 +66,7 @@
 #' @param ind.names either a character vector of names for the individuals to
 #' be plotted, or \code{FALSE} for no names. If \code{TRUE}, the row names of
 #' the first (or second) data matrix is used as names (see Details).
+#' @template arg/repel
 #' @param group factor indicating the group membership for each sample, useful
 #' for ellipse plots. Coded as default for the supervised methods \code{PLS-DA,
 #' SPLS-DA,sGCCDA}, but needs to be input for the unsupervised methods
@@ -160,6 +161,7 @@ check.input.plotIndiv <-
            blocks = NULL,
            # to choose which block data to plot, when using GCCA module
            ind.names = TRUE,
+           repel = repel,
            style = "ggplot2",
            # can choose between graphics, 3d, lattice or ggplot2
            #study = "global",
@@ -192,6 +194,7 @@ check.input.plotIndiv <-
     if (!style %in% c("ggplot2", "lattice", "graphics", "3d"))
       stop("'style' must be one of 'ggplot2', 'lattice', 'graphics' or '3d' .", call. = FALSE)
 
+
     #-- axes.box
     choices = c("box", "bbox", "both")
     axes.box = choices[pmatch(axes.box, choices)]

diff --git a/R/plotIndiv.pls.R b/R/plotIndiv.pls.R
@@ -9,6 +9,7 @@ plotIndiv.mixo_pls <-
              comp  = NULL,
              rep.space  = NULL,
              ind.names  = TRUE,
+             repel = FALSE,
              group,
              col.per.group,
              style = "ggplot2",
@@ -103,7 +104,7 @@ plotIndiv.mixo_pls <-
             stop("'background' must have been obtained with the 'background.predict' function")
 
         #-- check inputs
-        check  = check.input.plotIndiv(object = object, comp  = comp , blocks  = blocks, ind.names  = ind.names, 
+        check  = check.input.plotIndiv(object = object, comp  = comp , blocks  = blocks, ind.names  = ind.names, repel = repel,
                                        style = style, ellipse  = ellipse, ellipse.level  = ellipse.level, centroid = centroid, 
                                        star = star, legend = legend, X.label  = X.label, Y.label  = Y.label, Z.label  = Z.label, abline  = abline, 
                                        xlim  = xlim, ylim  = ylim, alpha = alpha, axes.box  = axes.box, plot_parameters = plot_parameters)
@@ -167,7 +168,7 @@ plotIndiv.mixo_pls <-
         #call plot module (ggplot2, lattice, graphics, 3d)
         res = internal_graphicModule(df = df, centroid = centroid, col.per.group = col.per.group, title = title,
                                      X.label = X.label, Y.label = Y.label, Z.label = Z.label, xlim = xlim, ylim = ylim, class.object = class(object),
-                                     display.names = display.names, legend = legend, abline = abline, star = star,
+                                     display.names = display.names, repel = repel, legend = legend, abline = abline, star = star,
                                      ellipse = ellipse, df.ellipse = df.ellipse, style = style, layout = layout, #missing.col = missing.col,
                                      axes.box = axes.box, plot_parameters = plot_parameters, alpha = alpha, background = background)
 

diff --git a/R/plotVar.R b/R/plotVar.R
@@ -50,6 +50,7 @@
 #' @param var.names either a character vector of names for the variables to be
 #' plotted, or \code{FALSE} for no names. If \code{TRUE}, the col names of the
 #' first (or second) data matrix is used as names.
+#' @template arg/repel
 #' @param blocks for an object of class \code{"rgcca"} or \code{"sgcca"}, a
 #' numerical vector indicating the block variables to display.
 #' @param X.label x axis titles.
@@ -109,6 +110,7 @@ plotVar <-
              comp.select = comp,
              plot = TRUE,
              var.names = NULL,
+             repel = FALSE,
              blocks = NULL,
              # to choose which block data to plot, when using GCCA module
              X.label = NULL,
@@ -673,14 +675,23 @@ plotVar <-
             for (i in levels(df$Block))
                 p = p + geom_point(data = subset(df, df$Block == i), size = 0, shape = 0)
 
+            .geom_text <- .get_geom_text(repel = repel, style = style)
+
             #-- Display sample or var.names
             for (i in seq_len(length(var.names))){
                 if (var.names[i]) {
-                    p = p + geom_text(data = df[c((ind.group[i] + 1) : ind.group[i + 1]), ],
+                    p = p + .geom_text(data = df[c((ind.group[i] + 1) : ind.group[i + 1]), ],
                                       label = df[c((ind.group[i] + 1) : ind.group[i + 1]), "names"],
                                       size = df[c((ind.group[i] + 1) : ind.group[i + 1]), "cex"],
                                       color = df[c((ind.group[i] + 1) : ind.group[i + 1]), "col"],
                                       fontface = df[c((ind.group[i] + 1) : ind.group[i + 1]), "font"])
+
+                    if (repel) {
+                        p = p + geom_point(data = df[c((ind.group[i] + 1) : ind.group[i + 1]), ],
+                                           size = 2,
+                                           shape = 16,
+                                           color = df[c((ind.group[i] + 1) : ind.group[i + 1]), "col"])
+                    }
                 } else {
                     p = p + geom_point(data = df[c((ind.group[i] + 1) : ind.group[i + 1]), ],
                                        size = df[c((ind.group[i] + 1) : ind.group[i + 1]), "cex"],

diff --git a/R/utils.R b/R/utils.R
@@ -665,3 +665,37 @@ mixo_gg.theme <- function(cex, x.angle = 90, background.fill = 'grey97', subtitl
     else
         sprintf("\033[33m%s\033[39m", char)
 }
+
+
+
+#' get geom_text based on repel arg
+#'
+#' @param repel Logical repel arg
+#' @param style Plot style. See ?plotIndiv
+#' @noRd
+#' @return geom_text function variation
+#' @keywords Internal
+.get_geom_text <- function(repel, style = 'ggplot2')
+{
+    if (isTRUE(repel))
+    {
+
+        if (style != 'ggplot2')
+            message("repel can only be used with style = 'ggplot2'")
+
+        repel <- FALSE
+        if(repel && requireNamespace("ggrepel", quietly = TRUE) == FALSE)
+            stop("the 'ggrepel' package is required with repel=TRUE", call. = FALSE)
+
+    }
+
+    if (repel)
+    {
+        geom_text_ <- ggplot2::geom_text
+    } else {
+        out <- ggrepel::geom_text_repel
+        formals(out)$max.overlaps <- Inf
+    }
+    geom_text_
+}
+
diff --git a/man-roxygen/arg/repel.R b/man-roxygen/arg/repel.R
@@ -0,0 +1,2 @@
+#' @param repel (if ind.names=TRUE), Logical indicating whether to spread the
+#' names away from each other in the plot.
diff --git a/man/plotIndiv.Rd b/man/plotIndiv.Rd
diff --git a/man/plotVar.Rd b/man/plotVar.Rd
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		#' @param repel (if ind.names=TRUE), Logical indicating whether to spread the
		#' names away from each other in the plot.