Adding odds ratios values and different colors in a ggplot graph in R

Question

I am trying to insert the Odds ratio values in the graph. I'm also trying to give different color to the shapes with significant Odds ratio. Significant Odds ratio are those whose confidence intervals does not include a value of 1. Can someone, please, help me with this?

My code exemple is:

df <- data.frame(yAxis = length(boxLabels):1,
boxOdds = c(2.23189,1.315737,1.22866,.8197413,.9802449,.9786673,.6559005,.5929812),
boxCILow = c(.7543566,1.016,.9674772,.6463458,.9643047,.864922,.4965308,.3572142),
boxCIHigh = c(6.603418,1.703902,1.560353,1.039654,.9964486,1.107371,.8664225,.9843584))

Ploting the graph

ggplot(df, aes(x = boxOdds, y = boxLabels)) +
  geom_vline(aes(xintercept = 1), size = .25, linetype = 'dashed') +
  geom_errorbarh(aes(xmax = boxCIHigh, xmin = boxCILow), size = .5, height = 
      .2, color = 'gray50') +
  geom_point(size = 3.5, color = 'orange') +
  theme_bw() +
  theme(panel.grid.minor = element_blank()) +
  scale_x_continuous(breaks = seq(0,7,1) ) +
  coord_trans(x = 'log10') +
  ylab('') +
  xlab('Odds ratio (log scale)') +
  annotate(geom = 'text', y =1.1, x = 3.5, label ='Model p < 0.001\nPseudo 
R^2 = 0.10', size = 3.5, hjust = 0) + ggtitle('My title')

The `boxLabels` variable is missing from your given data – RoB Feb 25 '21 at 15:22 — RoB, Feb 25 '21 at 15:22

RoB · Accepted Answer · 2021-02-25T15:40:18.643

I made a dummy variable for boxLabels since your code was missing it.

One thing to note for your future plots : define everything you need for the plot beforehand. Such as the a variable detailing whether or not your test is signifcant.

boxLabels <- letters[1:8] # dummy boxlabels variable

df <- data.frame(yAxis = length(boxLabels):1,
    boxOdds = c(2.23189,1.315737,1.22866,.8197413,.9802449,.9786673,.6559005,.5929812),
    boxCILow = c(.7543566,1.016,.9674772,.6463458,.9643047,.864922,.4965308,.3572142),
    boxCIHigh = c(6.603418,1.703902,1.560353,1.039654,.9964486,1.107371,.8664225,.9843584),
    boxLabels = boxLabels # Don't forget to actually put it in the dataframe if you use it in the plot.
) 

# Make a variable for whether your test is significant
df$isSignif <- df$boxCILow > 1 | df$boxCIHigh < 1

g <- ggplot(df, aes(x = boxOdds, y = boxLabels)) +
  geom_vline(aes(xintercept = 1), size = .25, linetype = 'dashed') +
  geom_errorbarh(aes(xmax = boxCIHigh, xmin = boxCILow), size = .5, height = 
      .2, color = 'gray50') +
  geom_point(aes(color = isSignif), size = 3.5) + ## Use the variable to define the color of your plot.
  theme_bw() +
  theme(panel.grid.minor = element_blank()) +
  scale_x_continuous(breaks = seq(0,7,1) ) +
  coord_trans(x = 'log10') +
  ylab('') +
  xlab('Odds ratio (log scale)') +
  annotate(geom = 'text', y =1.1, x = 3.5, label ='Model p < 0.001\nPseudo 
R^2 = 0.10', size = 3.5, hjust = 0) + ggtitle('My title')

# add the oddsRatio values to the plot
g <- g + geom_text(label=round(df$boxOdds, 2), nudge_y=0.25)
g

The only lines I changed from your code are those with a comment.

This outputs the following plot :

Sorry, the boxLabels variable was really missing from my data. Thank you very much for your attention and help. It worked nicely!!! — Baptista, Feb 26 '21 at 01:47
No problem! If your issue is resolved, then don't forget to accept the answer. — RoB, Feb 26 '21 at 08:23

Adding odds ratios values and different colors in a ggplot graph in R

1 Answers1