Plot Group-wise Bar Plots

Usage

groupwise_bar(
  data,
  group,
  trait,
  bar.border = TRUE,
  bar.alpha = 0.8,
  by = c("group", "trait"),
  relative.freq = FALSE,
  subset = c("facet", "none"),
  na.rm = TRUE,
  include.overall = TRUE,
  background.bar = TRUE,
  background.bar.alpha = 0.25,
  show.counts = TRUE,
  count.text.size = 3,
  position = c("dodge", "stack"),
  ncol = NULL,
  nrow = NULL
)

Arguments

data: The data as a data frame object. The data frame should possess columns specifying the group and trait.
group: Name of column specifying the group as a character string.
trait: Name of column specifying the trait as a character string.
bar.border: logical. If TRUE, bar border is also plotted. Default is TRUE.
bar.alpha: Alpha transparency for the group-wise bar plot.
by: The factor according to which the bars have to be grouped. Either "group" or "trait".
relative.freq: logical. If TRUE, the relative frequency or proportion is plotted instead of counts. Default is FALSE.
subset: The method for subsetting the plots according to the argument "group". Either "facet" for getting an plot using faceting in ggplot2 or "list" for getting a list of plots.
na.rm: logical. If TRUE, the NA factor levels are excluded from the plot. Default is TRUE.
include.overall: logical. If TRUE, the overall or total data is also plotted. Default is TRUE.
background.bar: logical. If TRUE, the overall data is plotted as a background bar plot when by = "group", include.overall = TRUE, and position = "dodge". Default is TRUE.
background.bar.alpha: Alpha transparency for the background bar plot.
show.counts: logical. If TRUE, group wise counts are plotted as a text annotation. Default is TRUE.
count.text.size: The size of the count text annotation.
position: Bar position adjustment. Either "dodge" or "stack".
ncol: Number of columns when subset = "facet".
nrow: Number of rows when subset = "facet".

Value

The group-wise bar plot as a ggplot2 plot grob or as a list of ggplot2 plot grobs.

Examples

library(agridat)
library(ggplot2)
library(patchwork)

soydata <- australia.soybean

clrs <- c("#B2182B", "#2166AC", "#009E53", "#E69F00", "gray25")
clrs_dark <- colorspace::darken(clrs, amount = 0.2)

soydata$lodging <- cut(soydata$lodging,
                       breaks = quantile(soydata$lodging, na.rm = TRUE),
                       include.lowest = TRUE)
levels(soydata$lodging) <- 1:4

# soydata[soydata$loc == "Nambour", ]$lodging <- NA
# #soydata[soydata$lodging == 1, ]$lodging
# soydata[!(is.na(soydata$lodging)) & soydata$lodging == 1, ]$lodging <- NA

# set.seed(123)
# ind <- sample(1:nrow(soydata), size = nrow(soydata) * 0.1, replace = FALSE)
# soydata[ind, ]$lodging <- NA

# Group-wise side-by-side bar plot with counts ----

outg_group_dodge_count <-
  groupwise_bar(data = soydata, group = "loc", trait = "lodging",
                bar.border = TRUE, by = "group",
                subset = "none", position = "dodge")

outg_group_dodge_count


outg_group_dodge_count +
  scale_fill_manual(values = clrs) +
  scale_colour_manual(values = clrs_dark)


outg_group_dodge_count_facet <-
  groupwise_bar(data = soydata, group = "loc", trait = "lodging",
                bar.border = TRUE, by = "group",
                subset = "facet", position = "dodge")

outg_group_dodge_count_facet


outg_group_dodge_count_facet +
  scale_fill_manual(values = clrs) +
  scale_colour_manual(values = clrs_dark)


outg_group_dodge_count_list <-
  groupwise_bar(data = soydata, group = "loc", trait = "lodging",
                bar.border = TRUE, by = "group",
                subset = "list", position = "dodge")

wrap_plots(outg_group_dodge_count_list, nrow = 2, guides = "collect")


outg_group_dodge_count_list <-
  lapply(seq_along(outg_group_dodge_count_list), function(i) {
    outg_group_dodge_count_list[[i]] +
      scale_fill_manual(values = clrs[i]) +
      scale_colour_manual(values = clrs_dark[i])
  })
#> Scale for fill is already present.
#> Adding another scale for fill, which will replace the existing scale.
#> Scale for colour is already present.
#> Adding another scale for colour, which will replace the existing scale.
#> Scale for fill is already present.
#> Adding another scale for fill, which will replace the existing scale.
#> Scale for colour is already present.
#> Adding another scale for colour, which will replace the existing scale.
#> Scale for fill is already present.
#> Adding another scale for fill, which will replace the existing scale.
#> Scale for colour is already present.
#> Adding another scale for colour, which will replace the existing scale.
#> Scale for fill is already present.
#> Adding another scale for fill, which will replace the existing scale.
#> Scale for colour is already present.
#> Adding another scale for colour, which will replace the existing scale.
#> Scale for fill is already present.
#> Adding another scale for fill, which will replace the existing scale.
#> Scale for colour is already present.
#> Adding another scale for colour, which will replace the existing scale.

wrap_plots(outg_group_dodge_count_list, nrow = 2, guides = "collect")


# Group-wise side-by-side bar plot with relative frequencies ----

outg_group_dodge_rfreq <-
  groupwise_bar(data = soydata, group = "loc", trait = "lodging",
                bar.border = TRUE, by = "group",
                relative.freq = TRUE,
                subset = "none", position = "dodge")

outg_group_dodge_rfreq


outg_group_dodge_rfreq +
  scale_fill_manual(values = clrs) +
  scale_colour_manual(values = clrs_dark)


outg_group_dodge_rfreq_facet <-
  groupwise_bar(data = soydata, group = "loc", trait = "lodging",
                bar.border = TRUE, by = "group",
                relative.freq = TRUE,
                subset = "facet", position = "dodge")

outg_group_dodge_rfreq_facet


outg_group_dodge_rfreq_facet +
  scale_fill_manual(values = clrs) +
  scale_colour_manual(values = clrs_dark)


outg_group_dodge_rfreq_list <-
  groupwise_bar(data = soydata, group = "loc", trait = "lodging",
                bar.border = TRUE, by = "group",
                relative.freq = TRUE,
                subset = "list", position = "dodge")

wrap_plots(outg_group_dodge_rfreq_list, nrow = 2, guides = "collect")


outg_group_dodge_rfreq_list <-
  lapply(seq_along(outg_group_dodge_rfreq_list), function(i) {
    outg_group_dodge_rfreq_list[[i]] +
      scale_fill_manual(values = clrs[i]) +
      scale_colour_manual(values = clrs_dark[i])
  })
#> Scale for fill is already present.
#> Adding another scale for fill, which will replace the existing scale.
#> Scale for colour is already present.
#> Adding another scale for colour, which will replace the existing scale.
#> Scale for fill is already present.
#> Adding another scale for fill, which will replace the existing scale.
#> Scale for colour is already present.
#> Adding another scale for colour, which will replace the existing scale.
#> Scale for fill is already present.
#> Adding another scale for fill, which will replace the existing scale.
#> Scale for colour is already present.
#> Adding another scale for colour, which will replace the existing scale.
#> Scale for fill is already present.
#> Adding another scale for fill, which will replace the existing scale.
#> Scale for colour is already present.
#> Adding another scale for colour, which will replace the existing scale.
#> Scale for fill is already present.
#> Adding another scale for fill, which will replace the existing scale.
#> Scale for colour is already present.
#> Adding another scale for colour, which will replace the existing scale.

wrap_plots(outg_group_dodge_rfreq_list, nrow = 2, guides = "collect")


# Group-wise stacked bar plot with counts ----

outg_group_stack_count <-
  groupwise_bar(data = soydata, group = "loc", trait = "lodging",
                bar.border = TRUE, by = "group",
                subset = "none", position = "stack")

outg_group_stack_count


outg_group_stack_count +
  scale_fill_manual(values = clrs) +
  scale_colour_manual(values = clrs_dark)


outg_group_stack_count_facet <-
  groupwise_bar(data = soydata, group = "loc", trait = "lodging",
                bar.border = TRUE, by = "group",
                subset = "facet", position = "stack")

outg_group_stack_count_facet


outg_group_stack_count_facet +
  scale_fill_manual(values = clrs) +
  scale_colour_manual(values = clrs_dark)


outg_group_stack_count_list <-
  groupwise_bar(data = soydata, group = "loc", trait = "lodging",
                bar.border = TRUE, by = "group",
                subset = "list", position = "stack")

wrap_plots(outg_group_stack_count_list, nrow = 2, guides = "collect")


outg_group_stack_count_list <-
  lapply(seq_along(outg_group_stack_count_list), function(i) {
    outg_group_stack_count_list[[i]] +
      scale_fill_manual(values = clrs) +
      scale_colour_manual(values = clrs_dark)
  })

wrap_plots(outg_group_stack_count_list, nrow = 2, guides = "collect")


# Group-wise stacked bar plot with relative frequencies ----

outg_group_stack_rfreq <-
  groupwise_bar(data = soydata, group = "loc", trait = "lodging",
                bar.border = TRUE, by = "group",
                relative.freq = TRUE,
                subset = "none", position = "stack")

outg_group_stack_rfreq


outg_group_stack_rfreq +
  scale_fill_manual(values = clrs) +
  scale_colour_manual(values = clrs_dark)


outg_group_stack_rfreq_facet <-
  groupwise_bar(data = soydata, group = "loc", trait = "lodging",
                bar.border = TRUE, by = "group",
                relative.freq = TRUE,
                subset = "facet", position = "stack")

outg_group_stack_rfreq_facet


outg_group_stack_rfreq_facet +
  scale_fill_manual(values = clrs) +
  scale_colour_manual(values = clrs_dark)


outg_group_stack_rfreq_list <-
  groupwise_bar(data = soydata, group = "loc", trait = "lodging",
                bar.border = TRUE, by = "group",
                relative.freq = TRUE,
                subset = "list", position = "stack")

wrap_plots(outg_group_stack_rfreq_list, nrow = 2, guides = "collect")


outg_group_stack_rfreq_list <-
  lapply(seq_along(outg_group_stack_rfreq_list), function(i) {
    outg_group_stack_rfreq_list[[i]] +
      scale_fill_manual(values = clrs) +
      scale_colour_manual(values = clrs_dark)
  })

wrap_plots(outg_group_stack_rfreq_list, nrow = 2, guides = "collect")



# Trait-wise side-by-side bar plot with counts ----

outg_trait_dodge_count <-
  groupwise_bar(data = soydata, group = "loc", trait = "lodging",
                bar.border = TRUE, by = "trait",
                subset = "none", position = "dodge")

outg_trait_dodge_count


outg_trait_dodge_count +
  scale_fill_manual(values = clrs) +
  scale_colour_manual(values = clrs_dark)


outg_trait_dodge_count_facet <-
  groupwise_bar(data = soydata, group = "loc", trait = "lodging",
                bar.border = TRUE, by = "trait",
                subset = "facet", position = "dodge")

outg_trait_dodge_count_facet


outg_trait_dodge_count_facet +
  scale_fill_manual(values = clrs) +
  scale_colour_manual(values = clrs_dark)


outg_trait_dodge_count_list <-
  groupwise_bar(data = soydata, group = "loc", trait = "lodging",
                bar.border = TRUE, by = "trait",
                subset = "list", position = "dodge")

wrap_plots(outg_trait_dodge_count_list, nrow = 2, guides = "collect")


outg_trait_dodge_count_list <-
  lapply(seq_along(outg_trait_dodge_count_list), function(i) {
    outg_trait_dodge_count_list[[i]] +
      scale_fill_manual(values = clrs[i]) +
      scale_colour_manual(values = clrs_dark[i])
  })
#> Scale for fill is already present.
#> Adding another scale for fill, which will replace the existing scale.
#> Scale for colour is already present.
#> Adding another scale for colour, which will replace the existing scale.
#> Scale for fill is already present.
#> Adding another scale for fill, which will replace the existing scale.
#> Scale for colour is already present.
#> Adding another scale for colour, which will replace the existing scale.
#> Scale for fill is already present.
#> Adding another scale for fill, which will replace the existing scale.
#> Scale for colour is already present.
#> Adding another scale for colour, which will replace the existing scale.
#> Scale for fill is already present.
#> Adding another scale for fill, which will replace the existing scale.
#> Scale for colour is already present.
#> Adding another scale for colour, which will replace the existing scale.

wrap_plots(outg_trait_dodge_count_list, nrow = 2, guides = "collect")


# Trait-wise side-by-side bar plot with relative frequencies ----

outg_trait_dodge_rfreq <-
  groupwise_bar(data = soydata, group = "loc", trait = "lodging",
                bar.border = TRUE, by = "trait",
                relative.freq = TRUE,
                subset = "none", position = "dodge")

outg_trait_dodge_rfreq


outg_trait_dodge_rfreq +
  scale_fill_manual(values = clrs) +
  scale_colour_manual(values = clrs_dark)


outg_trait_dodge_rfreq_facet <-
  groupwise_bar(data = soydata, group = "loc", trait = "lodging",
                bar.border = TRUE, by = "trait",
                relative.freq = TRUE,
                subset = "facet", position = "dodge")

outg_trait_dodge_rfreq_facet


outg_trait_dodge_rfreq_facet +
  scale_fill_manual(values = clrs) +
  scale_colour_manual(values = clrs_dark)


outg_trait_dodge_rfreq_list <-
  groupwise_bar(data = soydata, group = "loc", trait = "lodging",
                bar.border = TRUE, by = "trait",
                relative.freq = TRUE,
                subset = "list", position = "dodge")

wrap_plots(outg_trait_dodge_rfreq_list, nrow = 2, guides = "collect")


outg_trait_dodge_rfreq_list <-
  lapply(seq_along(outg_trait_dodge_rfreq_list), function(i) {
    outg_trait_dodge_rfreq_list[[i]] +
      scale_fill_manual(values = clrs[i]) +
      scale_colour_manual(values = clrs_dark[i])
  })
#> Scale for fill is already present.
#> Adding another scale for fill, which will replace the existing scale.
#> Scale for colour is already present.
#> Adding another scale for colour, which will replace the existing scale.
#> Scale for fill is already present.
#> Adding another scale for fill, which will replace the existing scale.
#> Scale for colour is already present.
#> Adding another scale for colour, which will replace the existing scale.
#> Scale for fill is already present.
#> Adding another scale for fill, which will replace the existing scale.
#> Scale for colour is already present.
#> Adding another scale for colour, which will replace the existing scale.
#> Scale for fill is already present.
#> Adding another scale for fill, which will replace the existing scale.
#> Scale for colour is already present.
#> Adding another scale for colour, which will replace the existing scale.

wrap_plots(outg_trait_dodge_rfreq_list, nrow = 2, guides = "collect")


# Trait-wise stacked bar plot with counts ----

outg_trait_stack_count <-
  groupwise_bar(data = soydata, group = "loc", trait = "lodging",
                bar.border = TRUE, by = "trait",
                subset = "none", position = "stack")

outg_trait_stack_count


outg_trait_stack_count +
  scale_fill_manual(values = clrs) +
  scale_colour_manual(values = clrs_dark)


outg_trait_stack_count_facet <-
  groupwise_bar(data = soydata, group = "loc", trait = "lodging",
                bar.border = TRUE, by = "trait",
                subset = "facet", position = "stack")

outg_trait_stack_count_facet


outg_trait_stack_count_facet +
  scale_fill_manual(values = clrs) +
  scale_colour_manual(values = clrs_dark)


outg_trait_stack_count_list <-
  groupwise_bar(data = soydata, group = "loc", trait = "lodging",
                bar.border = TRUE, by = "trait",
                subset = "list", position = "stack")

wrap_plots(outg_trait_stack_count_list, nrow = 2, guides = "collect")


outg_trait_stack_count_list <-
  lapply(seq_along(outg_trait_stack_count_list), function(i) {
    outg_trait_stack_count_list[[i]] +
      scale_fill_manual(values = clrs) +
      scale_colour_manual(values = clrs_dark)
  })

wrap_plots(outg_trait_stack_count_list, nrow = 2, guides = "collect")


# Trait-wise stacked bar plot with relative frequencies ----

outg_trait_stack_rfreq <-
  groupwise_bar(data = soydata, group = "loc", trait = "lodging",
                bar.border = TRUE, by = "trait",
                relative.freq = TRUE,
                subset = "none", position = "stack")

outg_trait_stack_rfreq


outg_trait_stack_rfreq +
  scale_fill_manual(values = clrs) +
  scale_colour_manual(values = clrs_dark)


outg_trait_stack_rfreq_facet <-
  groupwise_bar(data = soydata, group = "loc", trait = "lodging",
                bar.border = TRUE, by = "trait",
                relative.freq = TRUE,
                subset = "facet", position = "stack")

outg_trait_stack_rfreq_facet


outg_trait_stack_rfreq_facet +
  scale_fill_manual(values = clrs) +
  scale_colour_manual(values = clrs_dark)


outg_trait_stack_rfreq_list <-
  groupwise_bar(data = soydata, group = "loc", trait = "lodging",
                bar.border = TRUE, by = "trait",
                relative.freq = TRUE,
                subset = "list", position = "stack")

wrap_plots(outg_trait_stack_rfreq_list, nrow = 2, guides = "collect")


outg_trait_stack_rfreq_list <-
  lapply(seq_along(outg_trait_stack_rfreq_list), function(i) {
    outg_trait_stack_rfreq_list[[i]] +
      scale_fill_manual(values = clrs) +
      scale_colour_manual(values = clrs_dark)
  })

wrap_plots(outg_trait_stack_rfreq_list, nrow = 2, guides = "collect")