Keeping unused levels in ggplot2 bar plot does not work properly
R version 4.3.1 library(ggplot2) version 3.4.2
I want to use ggplot2 bar charts to display the percentage frequency of a particular concentration class. I have five concentration classes (=c1 with the options "1_", "2_", "3_", "4_", "5_") for which an event can occur "Early" (=c2 dichotomous with "yes" or "no") or "Late" (=c3 dichotomous with "yes" or "no").
To prevent bars from dropping in the diagram, I have set "scale_x_discrete (drop = FALSE)" in the ggplot.
If an event occurs in one, three, four or all five concentration classes, bar charts are drawn as I imagined them: no bar is drawn for the concentrations for which no event occurred, but all five concentration classes are displayed on the x-axis.
If an event occurs in only two concentration classes, then instead of the two thin bars at the respective concentrations, adjacent bold bars are drawn.
What is the reason for this problem and how can I solve it? Thank you very much in advance for any advice.
This is the code I used:
# build data.frame
c1 <- c("1_", "1_", "2_", "2_", "3_", "4_", "4_", "4_", "5_", "5_")
c2 <- c("yes", "yes", "no", "no", "no", "no", "no", "no", "no", "no")
c3 <- c("no", "no", "yes", "no", "yes", "yes", "no", "no", "no", "yes") # for five bars
c3 <- c("no", "no", "yes", "no", "yes", "no", "no", "no", "no", "yes") # for four bars
c3 <- c("no", "no", "yes", "no", "no", "no", "no", "no", "no", "yes") # for three bars
c3 <- c("no", "no", "no", "no", "no", "no", "no", "no", "no", "yes") # for two bars --> THIS is where the error occurs
c3 <- c("no", "no", "no", "no", "no", "no", "no", "no", "no", "no") # for one bars
dataf <- data.frame(c1, c2, c3)
dataf
# compilation of data + addition of column with event status + reduction of table to relevant columns
bp11 <- dataf %>% mutate(c.Compilation = case_when(c2 == "yes" ~ "EarlyEvent",
c3 == "yes" ~ "LateEvent")) %>%
select(c1, c.Compilation)
bp11
# insert number (n) and percentage share (prop)
bp22 <- bp11 %>% group_by(c1) %>% count(c.Compilation) %>% mutate(prop = n / sum(n) * 100)
# removal of NA
bp33 <- bp22[complete.cases(bp22$c.Compilation), ]
# specify factor level order "Groups"
bp33$c.Compilation = factor(bp33$c.Compilation, levels = c("LateEvent", "EarlyEvent"))
# specify factor level order "Concentration"
bp33$c1 = factor(bp33$c1, levels = c("1_", "2_", "3_", "4_", "5_"))
# calculate n of each concentration group
calcN <- table(bp11$c1)
calcN
# draw stacked barplot
ggplot(bp33,
aes(x = c1, y = prop, fill = c.Compilation)) +
geom_bar(stat = "identity",
position = "stack") +
labs(x = "Concentration (mg/L)",
y = "Event (%)",
fill = "Groups",
title = "Css") +
theme(axis.text = element_text(size = 15, face = "bold"),
axis.title = element_text(size = 15, face = "bold"),
legend.text = element_text(size = 15),
legend.title = element_text(size = 15),
plot.title = element_text(size = 20, hjust = 0.5)) +
theme(legend.position = c(.18, .84)) +
scale_x_discrete(breaks = c("1_", "2_", "3_", "4_", "5_"),
drop = FALSE) +
scale_y_continuous(limit = c(-1, 101), breaks = c(5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100)) +
annotate("text", x = c(0.9, 1.15), y = -1, label = c("n = ", calcN[c("1_")]), size = 5) +
annotate("text", x = c(1.9, 2.15), y = -1, label = c("n = ", calcN[c("2_")]), size = 5) +
annotate("text", x = c(2.9, 3.15), y = -1, label = c("n = ", calcN[c("3_")]), size = 5) +
annotate("text", x = c(3.9, 4.15), y = -1, label = c("n = ", calcN[c("4_")]), size = 5) +
annotate("text", x = c(4.9, 5.15), y = -1, label = c("n = ", calcN[c("5_")]), size = 5) +
scale_fill_grey(start = 0.6, end = 0)
This is the result I get when I run the code:
Solution
This looks like a bug to me (which after some testing occurs only with stat="identity" and when there are no adjacent categories).
NOTE: The issue was already reported and is fixed in the development version of ggplot2. (see below).
A workaround would be to manually complete your dataset using e.g. tidyr::complete:
library(ggplot2)
library(dplyr, warn = FALSE)
library(tidyr)
bp33_complete <- bp33 |>
ungroup() |>
complete(c1, c.Compilation, fill = list(prop = 0))
ggplot(
bp33_complete,
aes(x = c1, y = prop, fill = c.Compilation)
) +
geom_col() +
scale_x_discrete(
breaks = c("1_", "2_", "3_", "4_", "5_"),
drop = FALSE
) +
scale_y_continuous(
breaks = seq(5, 100, 5),
limits = c(-1, 101)
) +
labs(
x = "Concentration (mg/L)",
y = "Event (%)",
fill = "Groups",
title = "Css"
) +
theme(
axis.text = element_text(size = 15, face = "bold"),
axis.title = element_text(size = 15, face = "bold"),
legend.text = element_text(size = 15),
legend.title = element_text(size = 15),
plot.title = element_text(size = 20, hjust = 0.5)
) +
theme(legend.position = c(.18, .84)) +
geom_text(
aes(
label = after_stat(paste0("n = ", count)),
y = after_stat(-1),
fill = NULL
),
data = bp11,
stat = "count",
size = 5
) +
scale_fill_grey(start = 0.6, end = 0)
DATA
c1 <- c("1_", "1_", "2_", "2_", "3_", "4_", "4_", "4_", "5_", "5_")
c2 <- c("yes", "yes", "no", "no", "no", "no", "no", "no", "no", "no")
# for two bars --> THIS is where the error occurs
c3 <- c("no", "no", "no", "no", "no", "no", "no", "no", "no", "yes")
dataf <- data.frame(c1, c2, c3)
EDIT Here is a refactored code which uses only one dataset, keeps the NAs (but drops them for the geom_col) and uses geom_text with stat="summary" to compute the n= which should also work for cases with n=0.
library(ggplot2)
library(dplyr, warn = FALSE)
library(tidyr)
# Drop one c1 category
dataf <- filter(dataf, c1 != "4_")
bp33 <- dataf %>%
mutate(c.Compilation = case_when(
c2 == "yes" ~ "EarlyEvent",
c3 == "yes" ~ "LateEvent"
)) %>%
count(c1, c.Compilation) %>%
mutate(prop = n / sum(n) * 100, .by = c1) |>
mutate(
c.Compilation = factor(c.Compilation,
levels = c("LateEvent", "EarlyEvent")
),
c1 = factor(c1,
levels = c("1_", "2_", "3_", "4_", "5_")
)
) |>
complete(c1, c.Compilation, fill = list(prop = 0, n = 0))
ggplot(
bp33,
aes(x = c1, y = prop)
) +
geom_col(
data = ~ filter(.x, !is.na(c.Compilation)),
aes(fill = c.Compilation)
) +
scale_x_discrete(
breaks = c("1_", "2_", "3_", "4_", "5_"),
drop = FALSE
) +
scale_y_continuous(
breaks = seq(5, 100, 5),
limits = c(-1, 101)
) +
labs(
x = "Concentration (mg/L)",
y = "Event (%)",
fill = "Groups",
title = "Css"
) +
theme(
axis.text = element_text(size = 15, face = "bold"),
axis.title = element_text(size = 15, face = "bold"),
legend.text = element_text(size = 15),
legend.title = element_text(size = 15),
plot.title = element_text(size = 20, hjust = 0.5)
) +
theme(legend.position = c(.18, .84)) +
geom_text(
aes(
label = after_stat(paste0("n = ", y)),
y = stage(n, after_stat = -1),
fill = NULL,
group = c1
),
stat = "summary",
fun = sum,
size = 5
) +
scale_fill_grey(
start = 0.6, end = 0
)
Update The issue was already reported here and here and seems to be fixed in the development version of ggplot2:
Using ggplot2 3.4.4:
library(ggplot2)
packageVersion("ggplot2")
#> [1] '3.4.4'
dat <- data.frame(
x = factor(c("A", "E"), levels = LETTERS[1:5])
)
ggplot(dat, aes(x, y = 1)) +
geom_bar(stat = "identity") + # or geom_col
scale_x_discrete(drop = FALSE)
Created on 2023-12-30 with reprex v2.0.2
Using the development version:
library(ggplot2)
packageVersion("ggplot2")
#> [1] '3.4.4.9000'
dat <- data.frame(
x = factor(c("A", "E"), levels = LETTERS[1:5])
)
ggplot(dat, aes(x, y = 1)) +
geom_bar(stat = "identity") + # or geom_col
scale_x_discrete(drop = FALSE)
- Change Y intervals from 25% to 10%
- How to create a Marimekko/Mosaic plot in ggplot2
- Include code that does not run in Rpresentation Markdown
- How can I convert row names into the first column?
- How to add a ggplot2 subtitle with different size and colour?
- ggplot - making an internal pipeline within ggplot from object passed from previous pipeline
- Display bar as whole,value of bar as sum and remove as factor() from hover text
- highchart not rending in rshiny but is working in my directory
- How to listen to checkbox event that has been insert into ui using `insertUI` in Shiny-R
- Creating tooltip for radioGroupButtons while using bslib
- Reducing bootstrap table cell padding when using `bs_theme()`
- Rshiny popup won't appear under different tabs
- When I want to build a big matrix, my code becomes extremely slow. Why?
- Replace NA values in a data frame with the mean values of a variable depending on the rank of another variable
- Reshape data frame by row
- Write ZOO (XTS) object into CSV file by separating index column into two columns
- Pruning / Retrieving Nodes from a Tree Based on Parent / Child / Sibling Relationships
- Replace NA row with non-NA value from previous row and certain column
- Changing Values on the Same Column for Different DataFrames (in R)
- Binned Barplot in R
- Need a way of clumping columns together without trailing NAs and reversing the result
- How to use different parameters based on a vector for each iteration of lapply?
- Fit same model to many datasets in Python
- Why can't I iteratively add ggplot objects to a list?
- Problem with Plotting the dates on x axis for every timepoint in ggplot - and also some weird date conversion things (sidebar)
- Drawing state boundaries in county map in recent version
- How to replace and delete different underscore in a single name row
- Error package arrowR : read_parquet/open_dataset "Couldn't deserialize thrift: TProtocolException: Exceeded size limit"
- somatoChart in r (plot or ggplot)
- Selecting Flat Parts of a Curve