partykit - How to plot a glmtree without overlapping of terminal nodes?
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1
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I would like to plot a tree resulting from glmtree (partykit package). Unfortunately, the terminal nodes are overlapping and the labels of the graphs are no longer displayed properly.
The code that generates the tree is this one:
library(partykit)
library(aVirtualTwins)
data(sepsis)
attach(sepsis)
data <- cbind(y = survival, trt = as.factor(THERAPY), sepsis[,3:13])
formula <- as.formula(paste("y ~ trt", paste(names(sepsis[,3:13]),
collapse = " + "), sep = " | "))
fit <- glmtree(formula, data, family = binomial)
plot(fit)
detach(sepsis)
Is there a way to customize the output of plot() in order to avoid overlapping of the terminal nodes?
Here is a picture of what I mean:
r plot tree glm party
edited Nov 9 at 15:24
miselking
1,60841927
asked Nov 9 at 14:31
calcium238
84
add a comment |
up vote
1
down vote
favorite
I would like to plot a tree resulting from glmtree (partykit package). Unfortunately, the terminal nodes are overlapping and the labels of the graphs are no longer displayed properly.
The code that generates the tree is this one:
library(partykit)
library(aVirtualTwins)
data(sepsis)
attach(sepsis)
data <- cbind(y = survival, trt = as.factor(THERAPY), sepsis[,3:13])
formula <- as.formula(paste("y ~ trt", paste(names(sepsis[,3:13]),
collapse = " + "), sep = " | "))
fit <- glmtree(formula, data, family = binomial)
plot(fit)
detach(sepsis)
Is there a way to customize the output of plot() in order to avoid overlapping of the terminal nodes?
Here is a picture of what I mean:
r plot tree glm party
edited Nov 9 at 15:24
miselking
1,60841927
asked Nov 9 at 14:31
calcium238
84
add a comment |
up vote
1
down vote
favorite
up vote
1
down vote
favorite
I would like to plot a tree resulting from glmtree (partykit package). Unfortunately, the terminal nodes are overlapping and the labels of the graphs are no longer displayed properly.
The code that generates the tree is this one:
library(partykit)
library(aVirtualTwins)
data(sepsis)
attach(sepsis)
data <- cbind(y = survival, trt = as.factor(THERAPY), sepsis[,3:13])
formula <- as.formula(paste("y ~ trt", paste(names(sepsis[,3:13]),
collapse = " + "), sep = " | "))
fit <- glmtree(formula, data, family = binomial)
plot(fit)
detach(sepsis)
Is there a way to customize the output of plot() in order to avoid overlapping of the terminal nodes?
Here is a picture of what I mean:
r plot tree glm party
edited Nov 9 at 15:24
miselking
1,60841927
asked Nov 9 at 14:31
calcium238
84
I would like to plot a tree resulting from glmtree (partykit package). Unfortunately, the terminal nodes are overlapping and the labels of the graphs are no longer displayed properly.
The code that generates the tree is this one:
library(partykit)
library(aVirtualTwins)
data(sepsis)
attach(sepsis)
data <- cbind(y = survival, trt = as.factor(THERAPY), sepsis[,3:13])
formula <- as.formula(paste("y ~ trt", paste(names(sepsis[,3:13]),
collapse = " + "), sep = " | "))
fit <- glmtree(formula, data, family = binomial)
plot(fit)
detach(sepsis)
Is there a way to customize the output of plot() in order to avoid overlapping of the terminal nodes?
Here is a picture of what I mean:
r plot tree glm party
r plot tree glm party
edited Nov 9 at 15:24
miselking
1,60841927
asked Nov 9 at 14:31
calcium238
84
edited Nov 9 at 15:24
miselking
1,60841927
asked Nov 9 at 14:31
calcium238
84
edited Nov 9 at 15:24
miselking
1,60841927
edited Nov 9 at 15:24
miselking
1,60841927
edited Nov 9 at 15:24
miselking
1,60841927
1,60841927
asked Nov 9 at 14:31
calcium238
84
asked Nov 9 at 14:31
calcium238
84
asked Nov 9 at 14:31
calcium238
84
84
add a comment |
add a comment |
1 Answer
1
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oldest
votes
up vote
0
down vote
accepted
The plot() output for glmtree objects (and also other partykit objects) is customizable through panel functions for all aspects of the tree (inner nodes, terminal nodes, edges, ...). The panel function employed by default for this kind of tree is node_bivplot() which has a number of arguments that can be tweaked. See ?node_bivplot for details. The relevant option here is ylines that you can increase to 2, for example.
To pass arguments to the terminal panel functiontp_args can be used:
plot(fit, tp_args = list(ylines = 2))
answered Nov 9 at 22:29
Achim Zeileis
6,06111925
Thanks, Achim, for your support. Now I understand, how to pass arguments to the panel functions. Additionally, I changed some names of covariates and this is, what I came up with: plot(fit.glmtree, tp_args = list(ylines = 1, margins = c(1.5, 1.2, 1.5, 2.5)), ep_args = list(digits = 1))
– calcium238
Nov 12 at 7:24
Great, glad it could be solved. Could you please also accept the answer here on StackOverflow that it gets flagged as solved by the system?
– Achim Zeileis
Nov 12 at 9:37
add a comment |
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1 Answer
1
active
oldest
votes
1 Answer
1
active
oldest
votes
active
oldest
votes
active
oldest
votes
up vote
0
down vote
accepted
The plot() output for glmtree objects (and also other partykit objects) is customizable through panel functions for all aspects of the tree (inner nodes, terminal nodes, edges, ...). The panel function employed by default for this kind of tree is node_bivplot() which has a number of arguments that can be tweaked. See ?node_bivplot for details. The relevant option here is ylines that you can increase to 2, for example.
To pass arguments to the terminal panel functiontp_args can be used:
plot(fit, tp_args = list(ylines = 2))
answered Nov 9 at 22:29
Achim Zeileis
6,06111925
Thanks, Achim, for your support. Now I understand, how to pass arguments to the panel functions. Additionally, I changed some names of covariates and this is, what I came up with: plot(fit.glmtree, tp_args = list(ylines = 1, margins = c(1.5, 1.2, 1.5, 2.5)), ep_args = list(digits = 1))
– calcium238
Nov 12 at 7:24
Great, glad it could be solved. Could you please also accept the answer here on StackOverflow that it gets flagged as solved by the system?
– Achim Zeileis
Nov 12 at 9:37
add a comment |
up vote
0
down vote
accepted
The plot() output for glmtree objects (and also other partykit objects) is customizable through panel functions for all aspects of the tree (inner nodes, terminal nodes, edges, ...). The panel function employed by default for this kind of tree is node_bivplot() which has a number of arguments that can be tweaked. See ?node_bivplot for details. The relevant option here is ylines that you can increase to 2, for example.
To pass arguments to the terminal panel functiontp_args can be used:
plot(fit, tp_args = list(ylines = 2))
answered Nov 9 at 22:29
Achim Zeileis
6,06111925
Thanks, Achim, for your support. Now I understand, how to pass arguments to the panel functions. Additionally, I changed some names of covariates and this is, what I came up with: plot(fit.glmtree, tp_args = list(ylines = 1, margins = c(1.5, 1.2, 1.5, 2.5)), ep_args = list(digits = 1))
– calcium238
Nov 12 at 7:24
Great, glad it could be solved. Could you please also accept the answer here on StackOverflow that it gets flagged as solved by the system?
– Achim Zeileis
Nov 12 at 9:37
add a comment |
up vote
0
down vote
accepted
up vote
0
down vote
accepted
The plot() output for glmtree objects (and also other partykit objects) is customizable through panel functions for all aspects of the tree (inner nodes, terminal nodes, edges, ...). The panel function employed by default for this kind of tree is node_bivplot() which has a number of arguments that can be tweaked. See ?node_bivplot for details. The relevant option here is ylines that you can increase to 2, for example.
To pass arguments to the terminal panel functiontp_args can be used:
plot(fit, tp_args = list(ylines = 2))
answered Nov 9 at 22:29
Achim Zeileis
6,06111925
The plot() output for glmtree objects (and also other partykit objects) is customizable through panel functions for all aspects of the tree (inner nodes, terminal nodes, edges, ...). The panel function employed by default for this kind of tree is node_bivplot() which has a number of arguments that can be tweaked. See ?node_bivplot for details. The relevant option here is ylines that you can increase to 2, for example.
To pass arguments to the terminal panel functiontp_args can be used:
plot(fit, tp_args = list(ylines = 2))
answered Nov 9 at 22:29
Achim Zeileis
6,06111925
answered Nov 9 at 22:29
Achim Zeileis
6,06111925
answered Nov 9 at 22:29
Achim Zeileis
6,06111925
answered Nov 9 at 22:29
Achim Zeileis
6,06111925
6,06111925
Thanks, Achim, for your support. Now I understand, how to pass arguments to the panel functions. Additionally, I changed some names of covariates and this is, what I came up with: plot(fit.glmtree, tp_args = list(ylines = 1, margins = c(1.5, 1.2, 1.5, 2.5)), ep_args = list(digits = 1))
– calcium238
Nov 12 at 7:24
Great, glad it could be solved. Could you please also accept the answer here on StackOverflow that it gets flagged as solved by the system?
– Achim Zeileis
Nov 12 at 9:37
add a comment |
Thanks, Achim, for your support. Now I understand, how to pass arguments to the panel functions. Additionally, I changed some names of covariates and this is, what I came up with: plot(fit.glmtree, tp_args = list(ylines = 1, margins = c(1.5, 1.2, 1.5, 2.5)), ep_args = list(digits = 1))
– calcium238
Nov 12 at 7:24
Great, glad it could be solved. Could you please also accept the answer here on StackOverflow that it gets flagged as solved by the system?
– Achim Zeileis
Nov 12 at 9:37
Thanks, Achim, for your support. Now I understand, how to pass arguments to the panel functions. Additionally, I changed some names of covariates and this is, what I came up with: plot(fit.glmtree, tp_args = list(ylines = 1, margins = c(1.5, 1.2, 1.5, 2.5)), ep_args = list(digits = 1))
– calcium238
Nov 12 at 7:24
Thanks, Achim, for your support. Now I understand, how to pass arguments to the panel functions. Additionally, I changed some names of covariates and this is, what I came up with: plot(fit.glmtree, tp_args = list(ylines = 1, margins = c(1.5, 1.2, 1.5, 2.5)), ep_args = list(digits = 1))
– calcium238
Nov 12 at 7:24
Great, glad it could be solved. Could you please also accept the answer here on StackOverflow that it gets flagged as solved by the system?
– Achim Zeileis
Nov 12 at 9:37
Great, glad it could be solved. Could you please also accept the answer here on StackOverflow that it gets flagged as solved by the system?
– Achim Zeileis
Nov 12 at 9:37
add a comment |
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