Improving ggforest

[kassambara]

I just discovered the forestmodel package (https://github.com/NikNakk/forestmodel), which creates forest plots of the coefficients of models produced by lm, glm, survival::coxph

library("forestmodel")
library("survival")
library("dplyr")
pretty_lung <- lung %>%
  transmute(time,
            status,
            Age = age,
            Sex = factor(sex, labels = c("Male", "Female")),
            ECOG = factor(lung$ph.ecog),
            `Meal Cal` = meal.cal)

print(forest_model(coxph(Surv(time, status) ~ ., pretty_lung)))

@pbiecek : In ggforest(), I vote for staying focused on survival::coxph. But, how can we improve the output ? shoud we use internally the forestmodel package?

[pbiecek]

Cool, it works for lm and glm as well.
Will look into this.

[pbiecek]

It took me some time to look for some other ideas for forest model plots that will be as nice as the one generated by NikNakk. Will submit a new version of ggforest this weekend.

[kassambara]

Ok, great!!! Le samedi 1 avril 2017, Przemysław Biecek <notifications@github.com <javascript:_e(%7B%7D,'cvml','notifications@github.com');>> a écrit :

…

It took me some time to look for some other ideas for forest model plots that will be as nice as the one generated by NikNakk. Will submit a new version of ggforest this weekend. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#178 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ADKOy8s-JBAN8wrNpCqiTPh8fdn8IUYRks5rrgsUgaJpZM4Mmgec> .

[pbiecek]

The new version of ggforest looks like the figure below (will be uploaded soon, need some polishing)
I borrowed some ideas from forestmodel package. In addition to standard elements in the bottom-left corner there are some model statistics (AIC/n.events and others).

[kassambara]

Thank you @pbiecek for this great work!

Default text size in the ggforest() script is 0.7, some users might want to change this.
Suggestion: additional argument fontsize or labelsize or ...

I observed that, the hazard ratio axis ticks are not displayed sometimes. It seems to depend on the model. Do you have any idea?

For example,

1. In the example below, the axis ticks are displayed:

require("survival")
require("survminer")
model <- coxph( Surv(time, status) ~ sex+rx,
                data = colon )
ggforest(model)

2. But, in this second example, the ticks are not shown:

require("survival")
require("survminer")
model <- coxph( Surv(time, status) ~ sex+rx+adhere,
                data = colon )
ggforest(model)

[pbiecek]

Ticks are not displayed because the scale vary from 0.55 to 1.59 and the 'pretty printing' cannot find nice looking ticks in such narrow range.
One solution is to force the OX scale to be at least c(0.5, 2),
will add this if there are no other candidate solutions.

Having more graphical parameters exposed is a good idea, will do this.
However, the left panel is not a pure ggplot2 plot, so we cannot simply use theme parameter.

[pbiecek]

Ok, things are even stranger, since in the first plot the OX scale is more narrow.
Will look into this.

[pbiecek]

the problem was in using scale_x limits instead of coord_ limits
fixed in #182