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error when adding geom_signif to a plot #46
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Running into the same issue. Pretty sure it's related to #63, wasn't able to make that solution work for me though. |
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 infodevtools::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 ───────────────────────────────────────────────────────────────────
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#>
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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:
However, I still get the following error:
|
The original error is also explained here: |
Dear Constantin
Thank you very much for your package ggsignif, I very appreciate it.
I try to add results from chi-square test to a ggplot and it was mentioned, that I could use ggsignif:
https://stackoverflow.com/questions/51886623/compare-dependent-proportions-in-a-ggplot
Moreover I found your adivce to use geom_signif
#23
However, If i add this to my plot:
I get this error:
Warning: Ignoring unknown aesthetics: annotations, xmin, xmax, y_position
Error in FUN(X[[i]], ...) : object 'response' not found
If i leave out geom_signif(...) everything works.
Thank you for any advice,
Jacob
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