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Silence ggplot2 3.4.0 deprecation warnings. #36

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merged 2 commits into from
Jan 15, 2024
Merged

Silence ggplot2 3.4.0 deprecation warnings. #36

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c15fd4f
Silence ggplot2 3.4.0 deprecation warnings.
olivroy Jan 14, 2024
0b50b74
fix tiny mistake
olivroy Jan 14, 2024
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2 changes: 1 addition & 1 deletion DESCRIPTION
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Expand Up @@ -31,7 +31,7 @@ Imports:
GGally (>= 2.1.0),
ggbeeswarm,
ggh4x,
ggplot2 (>= 3.3.4),
ggplot2 (>= 3.4.0),
ggpmisc,
ggrepel (>= 0.7.0),
ggpubr,
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5 changes: 3 additions & 2 deletions NEWS.md
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Expand Up @@ -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
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12 changes: 6 additions & 6 deletions R/ggcontinuousexpdist.R
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Original file line number Diff line number Diff line change
Expand Up @@ -406,10 +406,10 @@ 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)
Expand All @@ -418,13 +418,13 @@ 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=""),")")
Expand Down Expand Up @@ -503,13 +503,13 @@ 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=""),")")
),
Expand Down
31 changes: 20 additions & 11 deletions R/ggkm.R
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Expand Up @@ -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

)

Expand All @@ -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

)

Expand Down Expand Up @@ -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(
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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) {

Expand Down Expand Up @@ -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) {
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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")

Expand Down
14 changes: 7 additions & 7 deletions R/gglogisticexpdist.R
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Expand Up @@ -494,10 +494,10 @@ 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)
Expand All @@ -507,13 +507,13 @@ 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=""),")")
Expand Down Expand Up @@ -591,19 +591,19 @@ 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)
Expand Down
20 changes: 10 additions & 10 deletions inst/shinyapp/server.R
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Expand Up @@ -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)
}


Expand Down Expand Up @@ -5921,7 +5921,7 @@ function(input, output, session) {
geom_line(
stat = "km",
trans = input$KMtrans ,
size = input$kmlinesize,
linewidth = input$kmlinesize,
alpha = input$kmlinealpha
)

Expand Down Expand Up @@ -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)


Expand Down
2 changes: 1 addition & 1 deletion man/geom_kmband.Rd
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2 changes: 1 addition & 1 deletion man/stat_kmband.Rd
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