Comments (4)
muhark
commented on May 28, 2024
Running into the same issue. Pretty sure it's related to #63, wasn't able to make that solution work for me though.
from ggsignif.
IndrajeetPatil
commented on May 28, 2024
Can reproduce:
library(tidyverse)
library(ggsignif)
library(ggalluvial)
df <- data.frame(
timepoint = rep(0:2, each = 10),
response = c("A", "B", "A", "A", "A", "A", "A", "A", "B", "B", "A", "A", "A", "A", "A", "A", "A", "B", "B", "B", "A", "B", "B", "B", "B", "B", "A", "B", "B", "B"),
variable = rep(c("var1", "var2"), each = 5, 3),
subject = rep(1:5, 6)
)
df$timepoint <- factor(df$timepoint,
level = c(1, 0, 2),
labels = c("method_A", "baseline", "method_B")
)
df %>%
add_count(timepoint, variable, response) %>%
add_count(timepoint, variable) %>%
mutate(freq = n / nn * 100) %>%
mutate(total = 1) -> df
#> Storing counts in `nn`, as `n` already present in input
#> ℹ Use `name = "new_name"` to pick a new name.
stats <- data.frame(xmax = c(rep(c("baseline", "method_B"), 2)))
stats %>%
mutate(xmin = as.factor(c(rep(c("method_A", "baseline"), 2)))) %>%
mutate(annotations = c("1", "0.2", "1", "0.5")) %>%
mutate(y_position = 5) %>%
mutate(variable = as.factor(c("var1", "var1", "var2", "var2"))) -> annotation_df
# without
ggplot(
df,
aes(
x = timepoint, stratum = response, alluvium = subject,
y = total,
fill = response, label = paste(freq, "%")
)
) +
geom_flow() +
geom_stratum(alpha = .5) +
geom_text(stat = "stratum", size = 3) +
theme(legend.position = "none") +
facet_wrap(~variable)
# with
ggplot(
df,
aes(
x = timepoint, stratum = response, alluvium = subject,
y = total,
fill = response, label = paste(freq, "%")
)
) +
geom_flow() +
geom_stratum(alpha = .5) +
geom_text(stat = "stratum", size = 3) +
theme(legend.position = "none") +
geom_signif(
data = annotation_df,
aes(annotations = annotations, xmin = xmin, xmax = xmax, y_position = y_position),
manual = TRUE
) +
facet_wrap(~variable)
#> Warning: Ignoring unknown aesthetics: annotations, xmin, xmax, y_position
#> Error in FUN(X[[i]], ...): object 'response' not found
Created on 2021-01-13 by the reprex package (v0.3.0)
Session info
devtools::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#> setting value
#> version R version 4.0.3 (2020-10-10)
#> os macOS Mojave 10.14.6
#> system x86_64, darwin17.0
#> ui X11
#> language (EN)
#> collate en_US.UTF-8
#> ctype en_US.UTF-8
#> tz Europe/Berlin
#> date 2021-01-13
#>
#> ─ Packages ───────────────────────────────────────────────────────────────────
#> package * version date lib source
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#>
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aubreyghoward
commented on May 28, 2024
I would like to add the the error in (FUN(X[[i]], ...) is caused by a lack of the specification on dataframe supplying the significance values for all required terms in the facted plot. In the above example, there is not a term in the significance dataframe for "response". This can be solved by supplying the discrete arguments for the comparisons you intend to plot. Please see this example code using diamonds below, which I hope clarifies the issue:
library(ggplot2)
library(ggsignif)
rm(list = ls())
diamonds.abbv <- diamonds[diamonds$clarity == c("I1","SI2"),]
df.sig <- data.frame( start = c(0.8, 1.2),
end = c(1.2,1.8),
y = c(3,3),
cut = c("Fair","Good"),
star = c("D", "E"),
label = c("#1", "#2"),
clarity = c("I1","I1"))
ggplot(data = diamonds.abbv, mapping = aes( x = color,
y = carat,
fill = clarity))+
geom_boxplot()+
facet_wrap(~cut)
ggplot(data = diamonds.abbv, mapping = aes( x = color,
y = carat,
fill = clarity))+
geom_boxplot()+
facet_wrap(~cut)+
geom_signif(data = df.sig, manual = TRUE,
mapping = aes(xmin = star, xmax = end, y_position = y, annotations = label))
##end run
However, I still get the following error:
[Warning message:
Ignoring unknown aesthetics: xmin, xmax, y_position, annotations ]
from ggsignif.
bersbersbers
commented on May 28, 2024
The original error is also explained here:
https://stackoverflow.com/a/40391432/880783
from ggsignif.
Related Issues (20)
- Error using facet_wrap & geom_signif : "Replacement has X rows..." HOT 2
- Customizing geom_signif with facet grid HOT 3
- Significance brackets HOT 1
- Figure out where the `WARNING`s and `NOTE`s in `R CMD check` are coming from HOT 1
- Manual vertical brackets do not work: "arguments imply differing number of rows" HOT 1
- Warning message: Ignoring unknown aesthetics: xmin, xmax, annotations, y_position HOT 3
- adding scale_y_log10 changes y-axis to a weird range
- geom_signif does not plot comparison on the facetted plot with free x scale HOT 2
- Where can we find the significance level in the ggplot object slots? HOT 1
- Rename default branch from `master` to `main` HOT 3
- CRAN release 0.6.4 HOT 3
- Correcting for multiple testing when using geom_signif HOT 5
- Feature request - add more distance between comparisons and data HOT 4
- geom_signif - all comparisons dissappear when one comparison has missings HOT 2
- Significance stars are misaligned when using "NS" as well
- ggsignif results don't match with anova significance HOT 1
- Use cross symbol when p <.10?
- what are * , ** , *** correspond if specific values by user is not given? HOT 1
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from ggsignif.