s6juncheng / ggpval Goto Github PK

When I run pval_star on your example data set (actually on any data set), it throws up the error:

Error in annotation[i, ] : incorrect number of dimensions

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Hello!
for example:

plane_p <- add_pval(plane_p, pairs = list(c(1, 2)), test = "t.test")

How should I specify the parameters used by t.test？
I want to specify

t.test(..., alternative = "less")

Thanks very much!

currently when using a facet with annotation it only uses the first one from the list.

add_pval(plt, pairs = list(c(1, 2)), annotation = list("Awesome1", "Awesome2"))

results in this figure:

Where Awesome2 is missing.

I quickly made a pkgdown website for ggpval, and I think it'll help increase its visibility. Here is a preview.

I can help you set up a custom url and to setup travis_ci() if you're interested.

Would be great to have an option for horizontal based plots

Detailed procedure: http://r-pkgs.had.co.nz/release.html

1. devtools::check()
2. bump version in DESCRIPTION
3. devtools::check_win_*()
4. devtools::check_win_devel()
5. devtools::release_checks()
6. devtools::check_rhub()
7. devtools::release()

Dear ggpval-team,

It is me again. I have another issue. I asked my question on Stackoverflow here: https://stackoverflow.com/questions/70740117/issues-with-ggpval-package-in-r

It seems that textsize is not working. Is that correct?

Thank you

Sarah

export function format_pval. If annotations are pvalue, add "parse=T"

Thanks for this package! I use {plotly} often using ggplotly(p) and was disappointed when {ggsignif} was unable to convert. Thankfully, {ggpval} has no such issue, however the styling of the text (italic 'P') does not carry over.

I appreciate that this isn't any fault of {ggpval} but in anticipation of this use case, how about an optional argument to disable styling of the text, so that it goes through ggplotly() verbatim?

# R.version.string
# [1] "R version 3.6.1 (2019-07-05)"
# packageVersion("ggpval")
# [1] ‘0.2.3’

library(ggplot2)
plt <- ggplot(mtcars, aes(factor(gear), mpg)) +
  geom_boxplot() + 
  geom_jitter()
p <- ggpval::add_pval(plt, pairs = list(c(1, 2)), test = "t.test")
plotly::ggplotly(p) 

# Create a dataframe
df <- data.frame(A = runif(5), 
                 B = runif(5), 
                 G = c("Group1", "Group2", "Group3", "Group4", "Group5")) 
# Melt the dataframe to be used for ggplot2
df_melt <- reshape2::melt(df, id.vars = "G")

# Create a list of p-values 
# Those values are the real ones that I have in my data
# I just modified them after the calculations by using case_when() with paste() as:
# (1) every p values lower than 0.001 is shown as "p < 0.001"
# (2) all the other values are shown as "p = xxx" 
# As shown on GitHub, annotation option needs a list
pvalues <- list("p < 0.001", "p < 0.001", "'p = 0.123'", "p = 0.813", "p = 0.043")

# Create the plot
library(ggplot2)
library(ggpval)
bar_plot <- ggplot(data = df_melt, aes(x = variable, y = value, fill = variable)) + geom_bar(stat = "identity", position = "dodge") +
  facet_grid(.~G)  +
  theme_bw() +
  scale_y_continuous(labels = scales::percent_format(), limits = c(0, 1.05)) 

# Add p-values
add_pval(bar_plot, pairs = list(c(1, 2)), annotation = pvalues)

Dear ggpval-team,

As you can see, Group 4 and Group 5 looks strange. Not Group 3 as I wrapped the quotations with the character string (I found that by chance as I got a parse issue 2 minutes before that part). My question is: can we avoid that extra step? Or am I doing something wrong?

EDIT: sorry, by also putting the character string for Group 4 and Group 5, it does not work for them...

Thank you for your help

Sarah

System information:
R Version: R version 4.1.1 (2021-08-10)
R Studio Version: 1.4.1717
OS: Ubuntu 20.04.3 LTS
Platform: x86_64-pc-linux-gnu (64-bit)