Comments (5)
There is currently no way to plot only brackets for significant differences. The idea is that you decide in the beginning which comparisons are interesting for you and this package helps you to show their comparison.
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There's a way to avoid printing "NS" for non-significant comparisons, but this won't prevent the lines from being drawn. Since you can define what symbols to use at each significance level, something like
map_signif_level=c("***"=0.001,"**"=0.01, "*"=0.05, " "=2)
will cause anything with p>0.05 to not print any text.
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What I did is to filter the data I pass to the annotations
argument, for example, a label
column, by p-value and set the uninteresting ones to NA
. Then they will not be drawn at all. (Maybe this was not possible in earlier versions.)
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Hi @Midnighter, could you please share how you did that? Thank you!
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Similarly to the advanced example at the bottom of https://const-ae.github.io/ggsignif/
I created a data frame using the pairwiseComparisons::pairwise_comparisons
function similarly to the following where group
is the variable for the comparison groups and measure
are the values.
annotation_df <- tbl %>%
pairwiseComparisons::pairwise_comparisons(
group,
measure
) %>%
dplyr::mutate(
groups = purrr::pmap(
.l = list(group1, group2), .f = c
),
label = round(p.value, 3)
) %>%
dplyr::arrange(group1) %>%
dplyr::filter(p.value < 0.05)
I then create a ggplot
to my liking and directly use the above table.
plot <- ggplot2::ggplot(...) +
...
if (nrow(annotation_df) > 0) {
plot + ggsignif::geom_signif(
comparisons = annotation_df$groups,
annotations = annotation_df$label,
na.rm = TRUE,
parse = TRUE
)
}
I've put this into convenient functions that I use many times in my project. That makes it a bit less painful to prepare the data in the right way.
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Related Issues (20)
- 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
- How do I hide the no significant (NS) comparisons?
- Adding significance bar on coupled boxplots
- FDR warning HOT 1
- Show exact p value in comparisons HOT 3
- ggsignif facetting issue - Missing significance labels in certain facets
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