guide_legend() fails to render vector shapes when overriding aesthetics
Closed this issue · 1 comments
nebetbastet commented
Hi,
Here is my code:
rm(list=ls())
shape_events=c(EV = 4, CC = 17, WW = 19, ZZ = 19)
library(ggplot2)
library(dplyr)
res<- structure(list(USUBJID = c("D", "D",
"D", "D", "D", "D",
"D", "D", "B", "B",
"B", "B", "B", "B",
"B", "B", "B", "B",
"B", "B", "B", "B",
"B", "B", "E", "E",
"E", "E", "E", "E",
"E", "E", "E", "E",
"E", "E", "E", "E",
"E", "E", "A", "A",
"A", "A", "A", "A",
"A", "A", "C", "C",
"C", "C", "C", "C",
"C", "C", "C", "C"
), TRTSTART = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1), TRTEND = c(43, 43, 43, 43, 43, 43, 43, 43, 98, 98, 98, 98,
98, 98, 98, 98, 98, 98, 98, 98, 98, 98, 98, 98, 100, 100, 100,
100, 100, 100, 100, 100, 100, 100, 100, 100, 100, 100, 100, 100,
30, 30, 30, 30, 30, 30, 30, 30, 43, 43, 43, 43, 43, 43, 43, 43,
43, 43), FUPEND = c(85, 85, 85, 85, 85, 85, 85, 85, 92, 92, 92,
92, 92, 92, 92, 92, 92, 92, 92, 92, 92, 92, 92, 92, NA, NA, NA,
NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA),
ARM = structure(c(4L, 2L, 4L, 2L, 4L, 4L, 2L, 2L, 3L, 2L,
3L, 2L, 3L, 2L, 3L, 3L, 3L, 3L, 3L, 2L, 2L, 2L, 2L, 2L, 3L,
2L, 3L, 2L, 3L, 2L, 3L, 3L, 3L, 3L, 3L, 2L, 2L, 2L, 2L, 2L,
1L, 2L, 1L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, 2L, 2L, 1L, 2L, 1L,
1L, 2L, 2L), levels = c("Y3", "Follow-up", "Y2", "Y1",
"CC", "WW", "WW", "ZZ", "EV"), class = "factor"),
EVENTDUR = c(43, 43, 43, 43, 1, 22, 1, 22, 22, 22, 84, 84,
98, 98, 43, 64, 85, 22, 1, 43, 64, 85, 22, 1, 46, 46, 85,
85, 100, 100, 1, 23, 44, 65, 86, 1, 23, 44, 65, 86, 2, 2,
39, 39, 1, 22, 1, 22, 2, 23, 2, 23, 43, 43, 1, 22, 1, 22),
EVENTCD = structure(c(8L, 8L, 10L, 10L, 9L, 9L, 9L, 9L, 6L,
6L, 8L, 8L, 10L, 10L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L,
9L, 7L, 7L, 8L, 8L, 10L, 10L, 9L, 9L, 9L, 9L, 9L, 9L, 9L,
9L, 9L, 9L, 5L, 5L, 8L, 8L, 9L, 9L, 9L, 9L, 6L, 6L, 6L, 6L,
10L, 10L, 9L, 9L, 9L, 9L), levels = c("Y3", "Follow-up",
"Y2", "Y1", "CC", "WW", "WW", "ZZ", "EV",
"EOT"), class = "factor"), ORDER = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L),
levels = c("1", "2", "3", "4", "5"), class = "factor"),
Legend_Group = structure(c(10L, 10L, 1L, 2L, 5L, 5L, 5L, 5L, 11L, 11L, 10L, 10L, 3L, 2L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 9L, 9L, 10L, 10L, 3L, 2L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 6L, 6L, 10L,10L, 5L, 5L, 5L, 5L, 11L, 11L, 11L, 11L, 4L, 2L, 5L, 5L, 5L, 5L), levels = c("Y1", "Follow-up", "Y2", "Y3", "EV", "CC", "CC beyond CC-period", "CC", "WW", "ZZ", "WW" ), class = "factor")), row.names = c("47", "471", "44", "441",
"45", "46", "451", "461", "11", "111", "17", "171", "10", "101",
"12", "13", "14", "15", "16", "121", "131", "141", "151", "161",
"70", "701", "69", "691", "63", "631", "64", "65", "66", "67",
"68", "641", "651", "661", "671", "681", "6", "610", "9", "91",
"7", "8", "710", "83", "40", "41", "401", "411", "39", "391",
"42", "43", "421", "431"), class = "data.frame")
cols_segment=NULL
cols_events=c("EV" = "black","CC" = "#a114a8","WW" = "#4634eb","ZZ" = "#E61A33")
### Graphical parameters #####
arms<-unique(res$ARM)
yores<-arms[arms!="Follow-up"]
# colors
cols_yores<- c(Y1 = "#CCCCFF", Y2 = "#33CCFF", Y3 = "#6666FF")
cols_segment<-c(cols_yores,"Follow-up" = "grey")
cols<-c(cols_segment,cols_events)
# shapes
shape_yores<-rep(NA,length(arms)) %>% setNames(arms)
shape_override <- c(shape_yores, shape_events)
# segments
shape_segments<-rep(1,length(arms)) %>% setNames(arms)
segment_events<-rep(NA,length(shape_events)) %>% setNames(names(shape_events))
segment_override<-c(shape_segments,segment_events)
# stroke
stroke_segments<-rep(NA,length(arms)) %>% setNames(arms)
stroke_events<-rep(2,length(shape_events)) %>% setNames(names(shape_events))
stroke_override<-c(stroke_segments,stroke_events)
# size
size_segments<-rep(2,length(arms)) %>% setNames(arms)
size_events<-rep(5,length(shape_events)) %>% setNames(names(shape_events))
size_override<-c(size_segments,size_events)
# Ordonner pour que les infusions soient à la fin (donc CCoix devant les ronds et carrés)
res$EVENTCD<-droplevels(res$EVENTCD)
levels<-levels(res$EVENTCD) %>% .[.!="EV"] %>% c(.,"EV")
res$EVENTCD<- factor(res$EVENTCD,levels=levels)
res<-res[order(res$EVENTCD),]
geometrics<-unique(c(as.character(res$ARM), levels))
cols<-cols[geometrics] %>% .[!is.na(names(.))]
shape_override<-shape_override[geometrics] %>% .[!is.na(names(.))]
segment_override<-segment_override[geometrics] %>% .[!is.na(names(.))]
stroke_override<-segment_override[geometrics] %>% .[!is.na(names(.))]
size_override<-size_override[geometrics] %>% .[!is.na(names(.))]
# Formatting ######
# je suis obligée de faire ça pour avoir une légende "fusionnée"
# ajouter EV et ZZ dans les "levels" de ARM
res$ARM<-factor(res$ARM, levels=names(cols))
res$EVENTCD<-factor(res$EVENTCD, levels=c(names(cols),"EOT"))
res <- res[order(res$ORDER),]
# Separating follow up and non follow up data
# for bars
res_bar<-res[(res$USUBJID %in% res$USUBJID[res$EVENTCD == "EOT"]),] %>%
.[.$ARM != "Follow-up",]
# for arrows
res_arrow<-res[(!res$USUBJID %in% res$USUBJID[res$EVENTCD == "EOT"]),]%>%
.[.$ARM != "Follow-up",]
# max days
maxDays<- max(res$TRTEND + res$FUPEND, na.rm = T) + 10
if (!is.finite(maxDays)) {
maxDays<-max(res$TRTEND, na.rm=TRUE) + 10
}
p<-ggplot(res, aes(y = forcats::fct_inorder(ORDER),
group = forcats::fct_inorder(ORDER))) +
geom_segment(data=res[res$ARM!="Follow-up",],
aes(x = TRTSTART, xend = TRTEND, y = forcats::fct_inorder(ORDER), color = ARM),
linewidth = 2) +
geom_segment(data=res[res$ARM=="Follow-up",],
aes(x = TRTEND, xend = TRTEND + FUPEND, y = forcats::fct_inorder(ORDER), color = ARM),
linewidth = 2) +
geom_segment(data = res_arrow,
aes(x = TRTEND, xend = TRTEND + 5, y = forcats::fct_inorder(ORDER), color = ARM),
arrow = arrow(type = "closed", length = unit(0.2, "inches")),
linewidth = 2, show.legend = FALSE) + # Exclude arrow from legend
geom_segment(data =res_bar,
aes(x = TRTEND, xend = TRTEND, y = forcats::fct_inorder(ORDER), color = ARM),
arrow = arrow(type = "open", length = unit(0.1, "inches"), angle = 90),
linewidth = 3, show.legend = FALSE) + # Exclude arrow from legend
geom_point(data = res[res$ARM!="Follow-up"&res$EVENTCD != "EOT"&!is.na(res$EVENTCD),],
aes(x = EVENTDUR, y = forcats::fct_inorder(ORDER),
color = EVENTCD, shape = EVENTCD),
size = 5, stroke = 2) +
# Colors
scale_color_manual(name = "Trial periods and events",
values = cols) +
# Shape
scale_shape_manual(name = "Trial periods and events",
values = shape_override)+
# One legend for shape and colors
guides(color = guide_legend(override.aes = list(stroke = stroke_override,
shape = shape_override,
linetype = segment_override,
size = size_override)),
shape = "none") +
# y-axis
scale_y_discrete(name = "",
labels = res$USUBJID) + # Display usubjid
# X-axis
scale_x_continuous(name = "Time (Days)") + # x-axis by cycle (21 days)
# Minimal theme
theme_minimal() +
# Personnalisation des axes et de la légende
theme(title = element_text(size = 14, face = "bold"),
axis.text.y = element_text(size = 12, face = "bold"), # Taille de l'axe Y
legend.position = "right", # Placer la légende à droite
legend.box = "vertical", # Légende empilée verticalement
plot.caption = element_text(margin = margin(t = 15),
face = "italic",
size = 8,
hjust = 0),
plot.caption.position = "plot")
p
which renders as
As you can see, the cross doesn't appear in the legend... :/
Now, if I replace only the second line of my code and that I give a solid shape to "EV":
shape_events=c(EV = 15, CC = 17, WW = 19, ZZ = 19)
I get that:
It appears in the legend.
It doesn't make sense to me, so I guess it's a bug.
Here is my SessionInfo :
R version 4.5.1 (2025-06-13 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 26100)
Matrix products: default
LAPACK version 3.12.1
locale:
[1] LC_COLLATE=French_France.utf8 LC_CTYPE=French_France.utf8 LC_MONETARY=French_France.utf8
[4] LC_NUMERIC=C LC_TIME=French_France.utf8
time zone: Europe/Paris
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] dplyr_1.1.4 ggplot2_4.0.0
loaded via a namespace (and not attached):
[1] labeling_0.4.3 RColorBrewer_1.1-3 R6_2.6.1 tidyselect_1.2.1 farver_2.1.2
[6] magrittr_2.0.3 gtable_0.3.6 glue_1.8.0 tibble_3.3.0 pkgconfig_2.0.3
[11] generics_0.1.4 lifecycle_1.0.4 cli_3.6.5 S7_0.2.0 scales_1.4.0
[16] grid_4.5.1 vctrs_0.6.5 withr_3.0.2 compiler_4.5.1 forcats_1.0.0
[21] rstudioapi_0.17.1 tools_4.5.1 pillar_1.11.0 rlang_1.1.6
Thank you in advance for your help and correction!
EDIT : No problem with ggplot2 version 3.5.0
teunbrand commented
You're setting a non-solid shape to have stroke = NA for the EV level through stroke_override. This seems like a user error and not a bug on ggplot2's part. I'd also like to mention that it is easier to diagnose issues with a minimal example.