Silence ggplot2 3.4.0 deprecation warnings. (#36)

* Silence ggplot2 3.4.0 deprecation warnings. * fix tiny mistake
smouksassi · Jan 15, 2024 · edadc12 · edadc12
1 parent 2580e95
commit edadc12
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -30,7 +30,7 @@ Imports:
     GGally (>= 2.1.0),
     ggbeeswarm,
     ggh4x,
-    ggplot2 (>= 3.3.4),
+    ggplot2 (>= 3.4.0),
     ggpmisc,
     ggrepel (>= 0.7.0),
     ggpubr,

diff --git a/NEWS.md b/NEWS.md
@@ -5,9 +5,10 @@
 * fixing error in aspect.ratio not numeric (was also fixed in ggplot2)
 * fixing other regressions with ggpairs color and group
 * added support of pasting values of two/three variables where it was just a placeholder
-* added function `ggkmrisktable` to add facetable risk tables, km and by ntiles split exposures
-* added function `gglogisticexpdist` and `ggcontinuousexpdist` to add facetable logistic/linear regression with exposures split to  ntiles with exposure distributions by dose/group and optional y axis projections
+* added function `ggkmrisktable()` to add facetable risk tables, km and by ntiles split exposures
+* added function `gglogisticexpdist()` and `ggcontinuousexpdist()` to add facetable logistic/linear regression with exposures split to  ntiles with exposure distributions by dose/group and optional y axis projections
 * added link to github pages in description thanks to @olivroy
+* Fix part of ggplot2 3.4.0 deprecation warnings. (#27, @olivroy)
 
 # ggquickeda 0.3.0
 * added options to drop levels for user discrete shape and linetype scales

diff --git a/R/ggcontinuousexpdist.R b/R/ggcontinuousexpdist.R
@@ -407,10 +407,10 @@ ggcontinuousexpdist <- function(data = effICGI,
                         ggplot2::aes(linetype = "Linear Fit 95% CI"))+
     ggplot2::geom_line(data = predict_by_endpoint_expname_dose,
                        ggplot2::aes_string(y = "yhat", col = color_fill),
-                       alpha = 0.4, size = 2)+
+                       alpha = 0.4, linewidth = 2)+
     ggplot2::geom_line(data = predict_by_endpoint_expname_dose2,
                        ggplot2::aes_string(y = "yhat", col = color_fill),
-                       alpha = 0.4, size = 2.5)+
+                       alpha = 0.4, linewidth = 2.5)+
     ggplot2::geom_point(data = predict_by_endpoint_expname,
                         ggplot2::aes_string(x = "medexp", y = "ymid50", col = color_fill),
                         alpha = 0.4, size = 5)
@@ -419,13 +419,13 @@ ggcontinuousexpdist <- function(data = effICGI,
   if(exposure_distribution=="lineranges") {
     lineranges_ypos <- as.character(lineranges_ypos)
     p1l <- p1 +
-      ggplot2::geom_linerange(data = data.long.summaries.dose, size = 2, alpha = 0.4,
+      ggplot2::geom_linerange(data = data.long.summaries.dose, linewidth = 2, alpha = 0.4,
                               ggplot2::aes_string(xmin = "quant_10", xmax = "quant_90",y = lineranges_ypos,
                                                   col = color_fill,
                                                   group=   paste0("interaction(",paste(as.character(c(DOSEinputvar,color_fill)) ,collapse=",",sep=""),")")
                               ),
       position = ggstance::position_dodgev(height = lineranges_dodge),inherit.aes = FALSE)+
-      ggplot2::geom_linerange(data = data.long.summaries.dose, size = 2.5, alpha = 0.4,
+      ggplot2::geom_linerange(data = data.long.summaries.dose, linewidth = 2.5, alpha = 0.4,
                               ggplot2::aes_string(xmin = "quant_25", xmax=  "quant_75", y = lineranges_ypos, 
                                                   col = color_fill,
                                                   group=   paste0("interaction(",paste(as.character(c(DOSEinputvar,color_fill)) ,collapse=",",sep=""),")")
@@ -504,13 +504,13 @@ ggcontinuousexpdist <- function(data = effICGI,
     yproj_xpos <- as.character(yproj_xpos)
 
     p2df <- p2d +
-      ggplot2::geom_linerange(data = predict_by_endpoint_expname, alpha = 0.4, size = 2,
+      ggplot2::geom_linerange(data = predict_by_endpoint_expname, alpha = 0.4, linewidth = 2,
                               ggplot2::aes_string(x = yproj_xpos, ymin = "ymid10", ymax = "ymid90",
                                                   col = color_fill,
                                                   group=   paste0("interaction(",paste(as.character(c(DOSEinputvar,color_fill)) ,collapse=",",sep=""),")")
                               ),
                               position = ggplot2::position_dodge(width = yproj_dodge), inherit.aes = FALSE)+
-      ggplot2::geom_linerange(data = predict_by_endpoint_expname, alpha = 0.4, size = 2.5,
+      ggplot2::geom_linerange(data = predict_by_endpoint_expname, alpha = 0.4, linewidth = 2.5,
                               ggplot2::aes_string(x = yproj_xpos, ymin = "ymid25", ymax = "ymid75", col= color_fill,
                                                   group=   paste0("interaction(",paste(as.character(c(DOSEinputvar,color_fill)) ,collapse=",",sep=""),")")
                               ),

diff --git a/R/ggkm.R b/R/ggkm.R
@@ -28,10 +28,14 @@ GeomKm <- ggplot2::ggproto("GeomKm", ggplot2::Geom,
                            },
 
                            required_aes = c("x", "y"),
-                           default_aes = ggplot2::aes(colour="black", fill="grey60", size=.75,
+                           default_aes = ggplot2::aes(colour="black", fill="grey60", linewidth = .75,
                                                       linetype=1, weight=1, alpha = 1),
-                           draw_key = ggplot2::draw_key_path
-
+                           draw_key = ggplot2::draw_key_path,
+                           # To allow using size in ggplot2 < 3.4.0
+                           non_missing_aes = "size",
+
+                           # Tell ggplot2 to perform automatic renaming
+                           rename_size = TRUE                    
 
 )
 
@@ -55,10 +59,16 @@ GeomKmband <- ggplot2::ggproto("GeomKmband", ggplot2::Geom,
                                },
 
                                required_aes = c("x", "ymin", "ymax"),
-                               default_aes = ggplot2::aes(colour="black", fill="grey60", size=.75,
+                               default_aes = ggplot2::aes(colour="black", fill="grey60", linewidth=.75,
                                                           linetype=1, weight=1, alpha=0.4),
 
-                               draw_key = ggplot2::draw_key_smooth
+                               draw_key = ggplot2::draw_key_smooth,
+
+                               # To allow using size in ggplot2 < 3.4.0 https://www.tidyverse.org/blog/2022/08/ggplot2-3-4-0-size-to-linewidth/
+                               non_missing_aes = "size",
+
+                               # Tell ggplot2 to perform automatic renaming
+                               rename_size = TRUE     
 
 )
 
@@ -94,7 +104,6 @@ GeomKmticks <- ggplot2::ggproto("GeomKmticks", ggplot2::Geom,
                                   }
 
                                 },
-
                                 required_aes = c("x", "y"),
                                 non_missing_aes = c("size", "shape"),
                                 default_aes = ggplot2::aes(
@@ -154,7 +163,7 @@ geom_km <- function(mapping = NULL, data = NULL, stat = "km",
 #'   \item \code{alpha}
 #'   \item \code{color}
 #'   \item \code{linetype}
-#'   \item \code{size}
+#'   \item \code{linewidth}
 #' }
 #'
 #' @inheritParams ggplot2::geom_point
@@ -229,7 +238,7 @@ geom_kmticks <- function(mapping = NULL, data = NULL, stat = "kmticks",
 #' @export
 
 StatKm <- ggplot2::ggproto("StatKm", ggplot2::Stat,
-
+                           dropped_aes = c("status"),
                            compute_group = function(data, scales, trans = scales::identity_trans(), firstx = 0, firsty = 1,
                                                     type = "kaplan-meier", start.time = 0) {
 
@@ -269,7 +278,7 @@ StatKm <- ggplot2::ggproto("StatKm", ggplot2::Stat,
 #' @export
 
 StatKmband <- ggplot2::ggproto("StatKmband", ggplot2::Stat,
-
+                               dropped_aes = "status",
                                compute_group = function(data, scales, trans = scales::identity_trans(), firstx = 0, firsty = 1,
                                                         type = "kaplan-meier", error = "greenwood", conf.type = "log",
                                                         conf.lower = "usual", start.time = 0, conf.int = 0.95) {
@@ -397,7 +406,7 @@ stat_km <- function(mapping = NULL, data = NULL, geom = "km",
 #'   \item \code{alpha}
 #'   \item \code{color}
 #'   \item \code{linetype}
-#'   \item \code{size}
+#'   \item \code{linewidth}
 #' }
 #'
 #' @inheritParams ggplot2::stat_identity
@@ -507,7 +516,7 @@ StatKmticks <- ggplot2::ggproto("StatKmticks", ggplot2::Stat,
                                   sf.df
 
                                 },
-
+                                dropped_aes = "status",
                                 default_aes = ggplot2::aes(y = ..survival.., x = ..time..),
                                 required_aes = c("time", "status")
 

diff --git a/R/gglogisticexpdist.R b/R/gglogisticexpdist.R
@@ -491,10 +491,10 @@ gglogisticexpdist <- function(data = effICGI,
                         ggplot2::aes(linetype = "Logistic Fit 95% CI"))+
     ggplot2::geom_line(data = predict_by_endpoint_expname_dose,
                        ggplot2::aes_string(y = "yhat", col = color_fill),
-                       alpha = 0.4, size = 2)+
+                       alpha = 0.4, linewidth = 2)+
     ggplot2::geom_line(data = predict_by_endpoint_expname_dose2,
                        ggplot2::aes_string(y = "yhat", col = color_fill),
-                       alpha = 0.4, size = 2.5)+
+                       alpha = 0.4, linewidth = 2.5)+
     ggplot2::geom_point(data = predict_by_endpoint_expname,
                         ggplot2::aes_string(x = "medexp", y = "ymid50", col = color_fill),
                         alpha = 0.4, size = 5)
@@ -504,13 +504,13 @@ gglogisticexpdist <- function(data = effICGI,
   if(exposure_distribution=="lineranges") {
     lineranges_ypos <- as.character(lineranges_ypos)
     p1l <- p1 +
-      ggplot2::geom_linerange(data = data.long.summaries.dose, size = 2, alpha = 0.4,
+      ggplot2::geom_linerange(data = data.long.summaries.dose, linewidth = 2, alpha = 0.4,
                               ggplot2::aes_string(xmin = "quant_10", xmax = "quant_90",y = lineranges_ypos,
                                                   col = color_fill,
                                                   group=   paste0("interaction(",paste(as.character(c(DOSEinputvar,color_fill)) ,collapse=",",sep=""),")")
                               ),
       position = ggstance::position_dodgev(height = lineranges_dodge),inherit.aes = FALSE)+
-      ggplot2::geom_linerange(data = data.long.summaries.dose, size = 2.5, alpha = 0.4,
+      ggplot2::geom_linerange(data = data.long.summaries.dose, linewidth = 2.5, alpha = 0.4,
                               ggplot2::aes_string(xmin = "quant_25", xmax=  "quant_75", y = lineranges_ypos, 
                                                   col = color_fill,
                                                   group=   paste0("interaction(",paste(as.character(c(DOSEinputvar,color_fill)) ,collapse=",",sep=""),")")
@@ -588,19 +588,19 @@ gglogisticexpdist <- function(data = effICGI,
     yproj_xpos <- as.character(yproj_xpos)
 
     p2df <- p2d +
-      ggplot2::geom_linerange(data = predict_by_endpoint_expname, alpha = 0.4, size = 2,
+      ggplot2::geom_linerange(data = predict_by_endpoint_expname, alpha = 0.4, linewidth = 2,
                               ggplot2::aes_string(x = yproj_xpos, ymin = "ymid10", ymax = "ymid90",
                                                   col = color_fill,
                                                   group=   paste0("interaction(",paste(as.character(c(DOSEinputvar,color_fill)) ,collapse=",",sep=""),")")
                               ),
                               position = ggplot2::position_dodge(width = yproj_dodge), inherit.aes = FALSE)+
-      ggplot2::geom_linerange(data = predict_by_endpoint_expname, alpha = 0.4, size = 2.5,
+      ggplot2::geom_linerange(data = predict_by_endpoint_expname, alpha = 0.4, linewidth = 2.5,
                               ggplot2::aes_string(x = yproj_xpos, ymin = "ymid25", ymax = "ymid75", col= color_fill,
                                                   group=   paste0("interaction(",paste(as.character(c(DOSEinputvar,color_fill)) ,collapse=",",sep=""),")")
                               ),
                               position = ggplot2::position_dodge(width = yproj_dodge), inherit.aes = FALSE)+
       ggplot2::geom_point(data=predict_by_endpoint_expname, alpha = 0.4, size = 3,
-                          ggplot2::aes_string(x = yproj_xpos, y = "ymid50", col = color_fill,
+                          ggplot2::aes_string(x = yproj_xpos, y = "ymid50", color = color_fill,
                                               group=   paste0("interaction(",paste(as.character(c(DOSEinputvar,color_fill)) ,collapse=",",sep=""),")")
                               ),
                               position = ggplot2::position_dodge(width = yproj_dodge), inherit.aes = FALSE)

diff --git a/inst/shinyapp/server.R b/inst/shinyapp/server.R
@@ -2931,29 +2931,29 @@ function(input, output, session) {
            p <- p + geom_density(aes_string(y=densitytype),
                                  alpha=input$densityalpha,
                                  adjust=input$densityadjust,
-                                 size = input$densitylinesize)
+                                 linewidth = input$densitylinesize)
        }
         if(input$densityignorelinetype && !input$densityaddition%in% c("None","histocount")) {
           p <- p + geom_density(aes_string(binwidth=input$histobinwidth,
                                            y=densitytype),
                                 alpha=input$densityalpha,
                                 adjust=input$densityadjust,
                                 linetype = input$densitylinetypes,
-                                size = input$densitylinesize)
+                                linewidth = input$densitylinesize)
         }
 
         if(!input$densityignorelinetype && input$densityaddition == "histocount" ) {
           p <- p + geom_density(aes(binwidth=input$histobinwidth, y=binwidth*..count..),
                                 alpha=input$densityalpha,
                                 adjust=input$densityadjust,
-                                size = input$densitylinesize)
+                                linewidth = input$densitylinesize)
         }
         if(input$densityignorelinetype && input$densityaddition=="histocount") {
           p <- p + geom_density(aes(binwidth=input$histobinwidth, y=binwidth*..count..),
                                 alpha=input$densityalpha,
                                 adjust=input$densityadjust,
                                 linetype = input$densitylinetypes,
-                                size = input$densitylinesize)
+                                linewidth = input$densitylinesize)
         }
 
 
@@ -5921,7 +5921,7 @@ function(input, output, session) {
               geom_line(
                 stat = "km",
                 trans = input$KMtrans ,
-                size = input$kmlinesize,
+                linewidth = input$kmlinesize,
                 alpha = input$kmlinealpha
               )
 
@@ -6698,23 +6698,23 @@ function(input, output, session) {
 
       if (input$customvline1)
         p <-    p +
-        geom_vline(xintercept=input$vline1,color=input$vlinecol1,linetype=input$vlinetype1,size=input$vlinesize1)
+        geom_vline(xintercept=input$vline1,color=input$vlinecol1,linetype=input$vlinetype1,linewidth=input$vlinesize1)
       if (input$customvline2)
         p <-    p +
-        geom_vline(xintercept=input$vline2,color=input$vlinecol2,linetype=input$vlinetype2,size=input$vlinesize2)      
+        geom_vline(xintercept=input$vline2,color=input$vlinecol2,linetype=input$vlinetype2,linewidth=input$vlinesize2)      
 
       if (input$customhline1)
         p <-    p +
-        geom_hline(yintercept=input$hline1,color=input$hlinecol1,linetype=input$hlinetype1,size=input$hlinesize1)
+        geom_hline(yintercept=input$hline1,color=input$hlinecol1,linetype=input$hlinetype1,linewidth=input$hlinesize1)
 
       if (input$customhline2)
         p <-    p +
-        geom_hline(yintercept=input$hline2,color=input$hlinecol2,linetype=input$hlinetype2,size=input$hlinesize2)     
+        geom_hline(yintercept=input$hline2,color=input$hlinecol2,linetype=input$hlinetype2,linewidth=input$hlinesize2)     
 
       if (input$identityline)
         p <-    p + geom_abline(intercept = 0, slope = 1,
                                 col = input$identitylinecol,
-                                size = input$identitylinesize,
+                                linewidth = input$identitylinesize,
                                 linetype = input$identitylinetype)  
 
 

diff --git a/man/geom_kmband.Rd b/man/geom_kmband.Rd
diff --git a/man/stat_kmband.Rd b/man/stat_kmband.Rd