M15a

Module 15a: ggpubr

library(ggplot2)
library(ggpubr)
library(dplyr)

## 
## Attaching package: 'dplyr'

## The following objects are masked from 'package:stats':
## 
##     filter, lag

## The following objects are masked from 'package:base':
## 
##     intersect, setdiff, setequal, union

gap = read.csv("gapminderData5.csv")
str(gap)

## 'data.frame':    1704 obs. of  6 variables:
##  $ country  : chr  "Afghanistan" "Afghanistan" "Afghanistan" "Afghanistan" ...
##  $ year     : int  1952 1957 1962 1967 1972 1977 1982 1987 1992 1997 ...
##  $ pop      : num  8425333 9240934 10267083 11537966 13079460 ...
##  $ continent: chr  "Asia" "Asia" "Asia" "Asia" ...
##  $ lifeExp  : num  28.8 30.3 32 34 36.1 ...
##  $ gdpPercap: num  779 821 853 836 740 ...

gap07 = gap %>% 
  filter(year == 2007 & continent != "Oceania")

Scatter plots

ggplot(gap07, aes(x = gdpPercap, y = lifeExp, col = continent)) +
  geom_point() + scale_x_log10("GDP per capita ($)") +
  scale_y_continuous("Life Expectancy (yrs)") + ggtitle("GapMinder Data 2007")

ggscatter(gap07, x = "gdpPercap", y = "lifeExp", col = "continent",
          xlab = "GDP per capita ($)", ylab = "Life expectancy (yrs)",
          main = "GapMinder Data 2007") +
  xscale("log10, .format = TRUE")

Histograms

gghistogram(gap07, x = "lifeExp", main = "GapMinder Life Expectancy")

## Warning: Using `bins = 30` by default. Pick better value with the argument
## `bins`.

gghistogram(gap07, x = "lifeExp", fill = "continent", 
            main = "GapMinder Life Expectancy")

## Warning: Using `bins = 30` by default. Pick better value with the argument
## `bins`.

Palettes

gghistogram(gap07, x = "lifeExp", fill = "continent", 
            main = "GapMinder Life Expectancy", palette = "npg")

## Warning: Using `bins = 30` by default. Pick better value with the argument
## `bins`.

Density plots

ggdensity(gap07, x = "lifeExp", fill = "continent",
          main = "GapMinder Life Expectancy", palette = "jco")

ggdensity(gap07, x = "lifeExp", fill = "continent",
          main = "GapMinder Life Expectany", palette = "jco",
          facet.by = "continent")

ggdensity(gap07, x = "lifeExp", fill = "continent",
          main = "GapMinder Life Expectancy", palette = "jco",
          facet.by = "continent",
          add = "median", rug = TRUE)

Violin plots

ggviolin(gap07, x = "continent", y = "lifeExp")

ggviolin(gap07, x = "continent", y = "lifeExp",
         fill = "continent", palette = "jco",
         add = c("boxplot", "jitter"),
         ylab = "Life expectancy (yrs)")

ggviolin(gap07, x = "continent", y = "lifeExp",
         fill = "continent", palette = "jco",
         add = c("boxplot", "jitter"),
         ylab = "Life expectancy (yrs)",
         rotate = TRUE)

Bar plots

ggbarplot(gap07, x = "country", y = "lifeExp")

ggbarplot(gap07,
          x = "country",
          y = "lifeExp",
          fill = "continent",
          palette = "jco",
          x.text.angle = 90,
          ylab = "Life expectancy (yrs)",
          xlab = "Country") +
  font("x.text", size = 4)

ggbarplot(gap07,
          x = "country",
          y = "lifeExp",
          fill = "continent",
          palette = "jco",
          sort.val = "desc",
          sort.by.groups = FALSE,
          x.text.angle = 90,
          ylab = "Life expectancy (yrs)",
          xlab = "Country") +
  font("x.text", size = 4)

ggdotchart(gap07,
           x = "country",
           y = "lifeExp",
           color = "continent",
           palette = "jco",
           sorting = "descending",
           rotate = TRUE,
           group = "continent",
           add = "segments",
           ylab = "Life expectancy (yrs)",
           xlab = "Country") +
  font("y.text", size = 4)

Adding comparisons to plots

gap_sub = gap %>%
  filter(continent %in% c("Asia", "Africa"),
         year %in% c(1957, 1982, 2007))
ggboxplot(gap_sub, x = "continent", y = "lifeExp",
          ylab = "Years", col = "continent", add = "jitter")

ggboxplot(gap_sub, x = "continent", y = "lifeExp",
          ylab = "Years", col = "continent", add = "jitter") +
  stat_compare_means(label.y = 90)

ggboxplot(gap_sub, x = "continent", y = "lifeExp", ylab = "Years",
          col = "continent", add = "jitter") + stat_compare_means(method = "t.test", label.y = 90)

ggboxplot(gap_sub, x = "continent", y = "lifeExp",
          ylab = "Years", col = "continent", add = "jitter", facet.by = "year") +
  stat_compare_means(method = "t.test", label.y = 90)

Multiple groups

ggboxplot(gap_sub, x = "year", y = "lifeExp") +
  stat_compare_means(label.y = 80, method = "anova")

comps = list( c('1957', '1982'),
              c('1957', '2007'),
              c('1982', '2007'))
comps

## [[1]]
## [1] "1957" "1982"
## 
## [[2]]
## [1] "1957" "2007"
## 
## [[3]]
## [1] "1982" "2007"

ggboxplot(gap_sub, x = "year", y = "lifeExp", ylab = "Years") +
  stat_compare_means(method = "t.test", comparisons = comps,
                     bracket.size = .6, size = 4)

ggboxplot(gap_sub, x = "year", y = "lifeExp", ylab = "Years") +
  stat_compare_means(method = "t.test", comparisons = comps,
                     bracket.size = .6, size = 4) +
  stat_compare_means(label.y = 110, method = "anova")

ggboxplot(gap_sub, x = "year", y = "lifeExp", ylab = "Years", facet.by = "continent") +
  stat_compare_means(method = "t.test", comparisons = comps,
                     bracket.size = .6, size = 4) +
  stat_compare_means(label.y = 110, method = "anova")

ggboxplot(gap_sub, x = "year", y = "lifeExp", ylab = "Years", facet.by = "continent") +
  stat_compare_means(method = "t.test", ref.group = "1957") +
  stat_compare_means(label.y = 110, method = "anova")

ggboxplot(gap_sub, x = "year", y = "lifeExp", ylab = "Years", facet.by = "continent") +
  stat_compare_means(label = "p.signif", method = "t.test",
                     ref.group = "1957") +
  stat_compare_means(label.y = 110, method = "anova")