coefplot in R; change CI line colours

Question

Hi I'm using coefplot function in r to plot out the coefficients from a generalized linear model. I would like to change the colour of the 95% CI lines to be different from the 50% CI lines. The colour parameters defaults the same colour for both the 95% and 50% CI lines.

coeff<-coefplot(model1,pointSize=5,color="black",fillColor="grey",lwdOuter = 1.2,lwdInner=2)

coeff + theme_bw() +
  theme(panel.grid.major=element_blank(),panel.grid.minor=element_blank()) +
  theme (axis.title.y  = element_text(size=16)) +
  theme(axis.title.x = element_text(size=16)) +
  scale_y_discrete(name="",labels=c("NDAA","GAP","SS","PS","LL")) +
  theme (axis.text.x  = element_text(size=16)) +
  theme(axis.text.x = element_text(size=16)) +
  scale_x_continuous(name="Regression Estimate") +
  labs(title = "") +
  coord_flip()

eipi10 · Accepted Answer · 2015-09-07T21:17:10.240

You could probably create your own version of a coefficient plot that meets your needs without too much trouble. Here's a ggplot2 example:

library(ggplot2)

# Create a model to plot
m1 = lm(mpg ~ wt + cyl + carb, data=mtcars)
coefs = as.data.frame(summary(m1)$coefficients[-1,1:2])
names(coefs)[2] = "se" 
coefs$vars = rownames(coefs)

ggplot(coefs, aes(vars, Estimate)) + 
  geom_hline(yintercept=0, lty=2, lwd=1, colour="grey50") +
  geom_errorbar(aes(ymin=Estimate - 1.96*se, ymax=Estimate + 1.96*se), 
                lwd=1, colour="red", width=0) +
  geom_errorbar(aes(ymin=Estimate - se, ymax=Estimate + se), 
                lwd=2.5, colour="blue", width=0) +
  geom_point(size=4, pch=21, fill="yellow") +
  theme_bw()

Another point is to use the `coefplot` output and not your own coefficients. `mm <- coefplot(model1,plot=FALSE)` then you use `"HighInner", "LowInner", "HighOuter`..` variables. Maybe you can keep this to the OP as an exercise. — agstudy, Sep 07 '15 at 21:22

score 1 · Answer 2 · answered Sep 07 '15 at 15:00

1

You can't easily change the color here. Unfortunately the package don't give access to set colors here.

Either you change the grobs colors using grid package or gTable. This is the dirty solution. It assume you know a little bit how to navigate in the ggplot tree objects ( gpath)
Or you add a new color parameter to buildPlotting.lm . You should recompile the package.

answered Sep 07 '15 at 15:00

agstudy

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Thanks agstudy. Was beginning to suspect something as you mentioned but wanted to confirm first. – Anand Roopsind Sep 07 '15 at 15:40

score 0 · Answer 3 · answered Jan 05 '18 at 11:46

I had the same problem. You can solve it within coefplot if you alter the individual ggplot2 layers.

coef <- coefplot(model = model1
     , color = "blue"
     ) +
      theme_bw() 
coef$layers[[2]] <- geom_errorbarh(stat="identity", position = "identity", na.rm = FALSE
                                    , color = "yellow"
                                    , size = 1
                                    , mapping = aes(xmin = LowOuter, xmax = HighOuter
                                                    , height = 0, linetype = Model 
                                    ))
coef$layers[[3]] <- geom_errorbarh(stat="identity", position = "identity", na.rm = FALSE
                                    , color = "red"
                                    , size = 2
                                    , mapping = aes(xmin = LowInner, xmax = HighInner
                                          , height = 0, linetype = Model
                                          ))
coef

coefplot image

coefplot in R; change CI line colours

3 Answers3