rggplot2plotsurvivalsurvminer
How to find a label in a gg plot object generated by ggforest() to edit its content?
I have generated a ggforest plot (packages: survival, survminer)
fit <- coxph(formula, data)
p <- ggforest(fit, data)
and want to edit (remove) the label "gASV11PFS" in the plot
I tried to find variable where the description is stored with str(p, max.level = NA) but it does not display this variable.
> str(p, max.level = NA)
List of 11
$ data : list()
..- attr(*, "class")= chr "waiver"
$ layers :List of 1
..$ :Classes 'LayerInstance', 'Layer', 'ggproto', 'gg' <ggproto object: Class LayerInstance, Layer, gg>
aes_params: list
compute_aesthetics: function
compute_geom_1: function
compute_geom_2: function
compute_position: function
compute_statistic: function
computed_geom_params: list
computed_mapping: NULL
computed_stat_params: list
constructor: call
data: data.frame
draw_geom: function
finish_statistics: function
geom: <ggproto object: Class GeomDrawGrob, GeomCustomAnn, Geom, gg>
aesthetics: function
default_aes: uneval
draw_group: function
draw_key: function
draw_layer: function
draw_panel: function
extra_params:
handle_na: function
non_missing_aes:
optional_aes:
parameters: function
rename_size: FALSE
required_aes:
setup_data: function
setup_params: function
use_defaults: function
super: <ggproto object: Class GeomCustomAnn, Geom, gg>
geom_params: list
inherit.aes: FALSE
layer_data: function
map_statistic: function
mapping: NULL
position: <ggproto object: Class PositionIdentity, Position, gg>
compute_layer: function
compute_panel: function
required_aes:
setup_data: function
setup_params: function
super: <ggproto object: Class Position, gg>
print: function
setup_layer: function
show.legend: NA
stat: <ggproto object: Class StatIdentity, Stat, gg>
aesthetics: function
compute_group: function
compute_layer: function
compute_panel: function
default_aes: uneval
dropped_aes:
extra_params: na.rm
finish_layer: function
non_missing_aes:
optional_aes:
parameters: function
required_aes:
retransform: TRUE
setup_data: function
setup_params: function
super: <ggproto object: Class Stat, gg>
stat_params: list
super: <ggproto object: Class Layer, gg>
$ scales :Classes 'ScalesList', 'ggproto', 'gg' <ggproto object: Class ScalesList, gg>
add: function
add_defaults: function
add_missing: function
backtransform_df: function
clone: function
find: function
get_scales: function
has_scale: function
input: function
map_df: function
n: function
non_position_scales: function
scales: list
train_df: function
transform_df: function
super: <ggproto object: Class ScalesList, gg>
$ guides :Classes 'Guides', 'ggproto', 'gg' <ggproto object: Class Guides, gg>
add: function
assemble: function
build: function
draw: function
get_custom: function
get_guide: function
get_params: function
get_position: function
guides: NULL
merge: function
missing: <ggproto object: Class GuideNone, Guide, gg>
add_title: function
arrange_layout: function
assemble_drawing: function
available_aes: any
build_decor: function
build_labels: function
build_ticks: function
build_title: function
draw: function
draw_early_exit: function
elements: list
extract_decor: function
extract_key: function
extract_params: function
get_layer_key: function
hashables: list
measure_grobs: function
merge: function
override_elements: function
params: list
process_layers: function
setup_elements: function
setup_params: function
train: function
transform: function
super: <ggproto object: Class GuideNone, Guide, gg>
package_box: function
print: function
process_layers: function
setup: function
subset_guides: function
train: function
update_params: function
super: <ggproto object: Class Guides, gg>
$ mapping : Named list()
..- attr(*, "class")= chr "uneval"
$ theme :List of 136
..$ line : list()
.. ..- attr(*, "class")= chr [1:2] "element_blank" "element"
..$ rect : list()
.. ..- attr(*, "class")= chr [1:2] "element_blank" "element"
..$ text :List of 11
.. ..$ family : chr ""
.. ..$ face : chr "plain"
.. ..$ colour : chr "black"
.. ..$ size : num 14
.. ..$ hjust : num 0.5
.. ..$ vjust : num 0.5
.. ..$ angle : num 0
.. ..$ lineheight : num 0.9
.. ..$ margin : 'margin' num [1:4] 0points 0points 0points 0points
.. .. ..- attr(*, "unit")= int 8
.. ..$ debug : logi FALSE
.. ..$ inherit.blank: logi TRUE
.. ..- attr(*, "class")= chr [1:2] "element_text" "element"
..$ title : NULL
..$ aspect.ratio : NULL
..$ axis.title : list()
.. ..- attr(*, "class")= chr [1:2] "element_blank" "element"
..$ axis.title.x : NULL
..$ axis.title.x.top : NULL
..$ axis.title.x.bottom : NULL
..$ axis.title.y : NULL
..$ axis.title.y.left : NULL
..$ axis.title.y.right : NULL
..$ axis.text : list()
.. ..- attr(*, "class")= chr [1:2] "element_blank" "element"
..$ axis.text.x : NULL
..$ axis.text.x.top : NULL
..$ axis.text.x.bottom : NULL
..$ axis.text.y : NULL
..$ axis.text.y.left : NULL
..$ axis.text.y.right : NULL
..$ axis.text.theta : NULL
..$ axis.text.r : NULL
..$ axis.ticks : list()
.. ..- attr(*, "class")= chr [1:2] "element_blank" "element"
..$ axis.ticks.x : NULL
..$ axis.ticks.x.top : NULL
..$ axis.ticks.x.bottom : NULL
..$ axis.ticks.y : NULL
..$ axis.ticks.y.left : NULL
..$ axis.ticks.y.right : NULL
..$ axis.ticks.theta : NULL
..$ axis.ticks.r : NULL
..$ axis.minor.ticks.x.top : NULL
..$ axis.minor.ticks.x.bottom : NULL
..$ axis.minor.ticks.y.left : NULL
..$ axis.minor.ticks.y.right : NULL
..$ axis.minor.ticks.theta : NULL
..$ axis.minor.ticks.r : NULL
..$ axis.ticks.length : 'simpleUnit' num 0points
.. ..- attr(*, "unit")= int 8
..$ axis.ticks.length.x : NULL
..$ axis.ticks.length.x.top : NULL
..$ axis.ticks.length.x.bottom : NULL
..$ axis.ticks.length.y : NULL
..$ axis.ticks.length.y.left : NULL
..$ axis.ticks.length.y.right : NULL
..$ axis.ticks.length.theta : NULL
..$ axis.ticks.length.r : NULL
..$ axis.minor.ticks.length : 'simpleUnit' num 0points
.. ..- attr(*, "unit")= int 8
..$ axis.minor.ticks.length.x : NULL
..$ axis.minor.ticks.length.x.top : NULL
..$ axis.minor.ticks.length.x.bottom: NULL
..$ axis.minor.ticks.length.y : NULL
..$ axis.minor.ticks.length.y.left : NULL
..$ axis.minor.ticks.length.y.right : NULL
..$ axis.minor.ticks.length.theta : NULL
..$ axis.minor.ticks.length.r : NULL
..$ axis.line : list()
.. ..- attr(*, "class")= chr [1:2] "element_blank" "element"
..$ axis.line.x : NULL
..$ axis.line.x.top : NULL
..$ axis.line.x.bottom : NULL
..$ axis.line.y : NULL
..$ axis.line.y.left : NULL
..$ axis.line.y.right : NULL
..$ axis.line.theta : NULL
..$ axis.line.r : NULL
..$ legend.background : list()
.. ..- attr(*, "class")= chr [1:2] "element_blank" "element"
..$ legend.margin : 'margin' num [1:4] 0points 0points 0points 0points
.. ..- attr(*, "unit")= int 8
..$ legend.spacing : 'simpleUnit' num 14points
.. ..- attr(*, "unit")= int 8
..$ legend.spacing.x : NULL
..$ legend.spacing.y : NULL
..$ legend.key : list()
.. ..- attr(*, "class")= chr [1:2] "element_blank" "element"
..$ legend.key.size : 'simpleUnit' num 15.4points
.. ..- attr(*, "unit")= int 8
..$ legend.key.height : NULL
..$ legend.key.width : NULL
..$ legend.key.spacing : 'simpleUnit' num 7points
.. ..- attr(*, "unit")= int 8
..$ legend.key.spacing.x : NULL
..$ legend.key.spacing.y : NULL
..$ legend.frame : NULL
..$ legend.ticks : NULL
..$ legend.ticks.length : 'rel' num 0.2
..$ legend.axis.line : NULL
..$ legend.text :List of 11
.. ..$ family : NULL
.. ..$ face : NULL
.. ..$ colour : NULL
.. ..$ size : 'rel' num 0.857
.. ..$ hjust : NULL
.. ..$ vjust : NULL
.. ..$ angle : NULL
.. ..$ lineheight : NULL
.. ..$ margin : NULL
.. ..$ debug : NULL
.. ..$ inherit.blank: logi TRUE
.. ..- attr(*, "class")= chr [1:2] "element_text" "element"
..$ legend.text.position : NULL
..$ legend.title :List of 11
.. ..$ family : NULL
.. ..$ face : NULL
.. ..$ colour : NULL
.. ..$ size : NULL
.. ..$ hjust : num 0
.. ..$ vjust : NULL
.. ..$ angle : NULL
.. ..$ lineheight : NULL
.. ..$ margin : NULL
.. ..$ debug : NULL
.. ..$ inherit.blank: logi TRUE
.. ..- attr(*, "class")= chr [1:2] "element_text" "element"
..$ legend.title.position : NULL
..$ legend.position : chr "none"
..$ legend.position.inside : NULL
..$ legend.direction : NULL
..$ legend.byrow : NULL
..$ legend.justification : chr "center"
..$ legend.justification.top : NULL
..$ legend.justification.bottom : NULL
..$ legend.justification.left : NULL
..$ legend.justification.right : NULL
..$ legend.justification.inside : NULL
..$ legend.location : NULL
..$ legend.box : NULL
..$ legend.box.just : NULL
..$ legend.box.margin : 'margin' num [1:4] 0points 0points 0points 0points
.. ..- attr(*, "unit")= int 8
..$ legend.box.background : list()
.. ..- attr(*, "class")= chr [1:2] "element_blank" "element"
..$ legend.box.spacing : 'simpleUnit' num 14points
.. ..- attr(*, "unit")= int 8
.. [list output truncated]
..- attr(*, "class")= chr [1:2] "theme" "gg"
..- attr(*, "complete")= logi TRUE
..- attr(*, "validate")= logi TRUE
$ coordinates:Classes 'CoordCartesian', 'Coord', 'ggproto', 'gg' <ggproto object: Class CoordCartesian, Coord, gg>
aspect: function
backtransform_range: function
clip: off
default: FALSE
distance: function
expand: FALSE
is_free: function
is_linear: function
labels: function
limits: list
modify_scales: function
range: function
render_axis_h: function
render_axis_v: function
render_bg: function
render_fg: function
setup_data: function
setup_layout: function
setup_panel_guides: function
setup_panel_params: function
setup_params: function
train_panel_guides: function
transform: function
super: <ggproto object: Class CoordCartesian, Coord, gg>
$ facet :Classes 'FacetNull', 'Facet', 'ggproto', 'gg' <ggproto object: Class FacetNull, Facet, gg>
compute_layout: function
draw_back: function
draw_front: function
draw_labels: function
draw_panels: function
finish_data: function
init_scales: function
map_data: function
params: list
setup_data: function
setup_params: function
shrink: TRUE
train_scales: function
vars: function
super: <ggproto object: Class FacetNull, Facet, gg>
$ plot_env :<environment: 0x7fbdc486a828>
$ layout :Classes 'Layout', 'ggproto', 'gg' <ggproto object: Class Layout, gg>
coord: NULL
coord_params: list
facet: NULL
facet_params: list
finish_data: function
get_scales: function
layout: NULL
map_position: function
panel_params: NULL
panel_scales_x: NULL
panel_scales_y: NULL
render: function
render_labels: function
reset_scales: function
resolve_label: function
setup: function
setup_panel_guides: function
setup_panel_params: function
train_position: function
super: <ggproto object: Class Layout, gg>
$ labels : list()
- attr(*, "class")= chr [1:2] "gg" "ggplot"
How to find where the label is stored and edit it?
I tried also:
p + geom_label(show.legend = NA)
p + geom_text(show.legend = NA)
but it doesn't change anything.
As an example you can try:
fit <- coxph(Surv(time, status) ~ age, data = lung)
p <- ggforest(fit, data = lung)
p
and in the example the label "age" is to be edited in p
Solution
It's much easier to just change it on the data. Adapting the example from ggforest's help:
# Original
model <- coxph( Surv(time, status) ~ sex + rx + adhere, data = colon )
ggforest(model)
# Edited
names(colon)[4] <- "Lorem ipsum"
model <- coxph( Surv(time, status) ~ `Lorem ipsum` + rx + adhere, data = colon )
ggforest(model)
If you want to remove the label altogether, just rename the variable to " ":
names(colon)[4] <- " "
model <- coxph(Surv(time, status) ~ ` ` + rx + adhere, data = colon)
ggforest(model)
And if you want to remove multiple labels, rename multiple variables, with a different number of spaces for each:
names(colon)[4] <- " "
names(colon)[3] <- " "
names(colon)[8] <- " "
model <- coxph(Surv(time, status) ~ ` ` + ` ` + ` `, data = colon)
ggforest(model)
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