ggsignif | Easily add significance brackets to your ggplots | Data Visualization library
kandi X-RAY | ggsignif Summary
kandi X-RAY | ggsignif Summary
This package provides an easy way to indicate if two groups are significantly different. Commonly this is shown by a bar on top connecting the groups of interest which itself is annotated with the level of significance (NS, *, **, ***). The package provides a single layer (geom_signif) that takes the groups for comparison and the test (t.test, wilcox etc.) and adds the annotation to the plot.
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QUESTION
I am working on creating a basic boxplot with significance level bars (as showed here: How to draw the boxplot with significant level?)
The data I use is as follows:
title1 title2 value 1 A 8.88 2 A 5.84 3 A 13.28 4 A 16.89 1 B 21.39 2 B 20.77 3 B 28.03 4 B 19.78 1 C 28.89 2 C 35.41 3 C 37.47 4 C 50.11 1 D 50.84 2 D 53.21 3 D 46.47 4 D 45.03With the following code, creating the boxplot works fine. For the significance bars, I want to use paired t tests like title2=A vs. title2=B, with the two rows with title1=1 being a pair and so on.
In R, I entered the following command, but it yields different results for p. For instance, the p-value for A vs. D should be 0.003, but R yields 2.8e-05. What is the correct syntax for a paired t test?
...ANSWER
Answered 2022-Apr-15 at 01:11ggsignif
is computing the unpaired t-test, and I think you want the paired test. Luckily geom_signif
has a test.args
argument, which will allow you to pass paired = TRUE
to the geom:
QUESTION
I am trying to create a faceted boxplot with significance levels indicated as asterisks like '***'. The problem is, I am getting an error when trying to add the geom_signif layer.
Warning message: Ignoring unknown aesthetics: xmin, xmax, annotations, y_position, map_signif_level
This is my data
...ANSWER
Answered 2021-Nov-30 at 12:14I see several things.
Your p.adj is 1 all the time. So I can't create a label with *
Although you are receiving some warnings I am not receiving any error and the code is doing what I expected.
You can resize the ylim and define the height of the labels.
library(tidyverse) library(ggsignif) library(ggpubr)
QUESTION
I am trying to show the significance levels within a group consisting of two factors, but I seem to always get the significance levels between groups which is not what I want.
...ANSWER
Answered 2021-Nov-26 at 17:15Facets don't seem to work with {ggsignif}, but you could fake them, by looping over your dates, and then patching the plots together.
Below one way
QUESTION
ANSWER
Answered 2021-Oct-01 at 05:31Just add additional values to arguments in geom_signif
QUESTION
How could I test differences between boxplots x='a' and x='b', both being group='g1', and then between boxplots x='a' and x='b' both being group='g2'?
...ANSWER
Answered 2021-Sep-27 at 11:23One way would be to use an interaction between the x
and group
variables:
QUESTION
ANSWER
Answered 2021-Sep-15 at 19:40The issue is that geom_signif
inherits the global aesthetics you set inside ggplot()
. In particular, as you set fill=Follow
ggplot is expecting a variable with this name in the dataframe you passed via the data
argument of geom_signif
.
One option to solve this issue would be to make fill=Follow
a local aesthetic to geom_col
which also requires to map Follow
on the group aes
inside geom_text
.
QUESTION
EDITED
I was using the ggsignif package in a totally WRONG way: I didn't want to calculate significance values from the barplot but I just wanted to draw on the barplot the ones I already had from a separate analysis. To do this, this video helped me A LOT https://www.youtube.com/watch?v=30mqU2vcx68
OLD QUESTION
Hello, I'd like to ask a question about the ggsignif package in the R software. I want to display significant stars in top of paired bar graphs using facet_wrap and I'm following this thread Using ggsignif with grouped bar graphs and facet_wrap not working but I cannot apply the same code to my graph. As in the image I attach, I'd like to make comparisons between bars as I drew, but I don't know how to define the data I'm comparing.
I used this code to build my graph:
...ANSWER
Answered 2021-Sep-08 at 08:14Significance refers to a distribution requiring many values per group. But for each group (e.g. S1-green-A) there is only one value in your dataset. Thus you draw a barplot and not a boxplot. You can group more values together e.g. by ignoring the color:
QUESTION
I am creating a ridge plot to compare a few groups (using ggridges package) and would like to add significance brackets to show comparisons between some group levels (using ggsignif package).
But this doesn't seem to work because the computation fails in stat_ggsignif
.
Here is a reproducible example:
...ANSWER
Answered 2021-Aug-02 at 13:11I did not manage to combine A) geom_density_ridges and B) geom_signif. The reason is that (A) requires numerical variable as x and categories as y, while (B) requires numerical variable as y and categories as x. And I have not managed to overwrite this behaviour. But I assume that you have chosen ridge_plots over simple boxplots as you are interested in a more informative visualization of the distribution. To do so, there is a much better solution than ridge_plots, the so called violin plots. See below a standard boxplot (with labelled significance):
QUESTION
I have data as follows, to which I am trying to add p-values:
...ANSWER
Answered 2021-Jul-20 at 07:09Thanks for clarifying your expected outcome. Here is one way to include geom_signif()
annotations without altering the original plot:
QUESTION
I have data as follows:
...ANSWER
Answered 2021-Jul-16 at 08:53If you really want to do that (which I would advise against), you can make your x-variable a factor and set the levels to include a blank observation; add a blank observation with that level; and plot.
For example:
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