comparison among the accumulation density curves
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3.8 years ago
Kai_Qi ▴ 130

I have a dataframe with the following structure

> str(mydata12)
    'data.frame':   228459 obs. of  2 variables:
     $ intron_length: num  0.787 0.799 2.311 2.396 1.77 ...
     $ intron_type  : Factor w/ 3 levels "All_intron","All_retained_intron",..: 1 1 1 1 1 1 1 1 1 1 ...

I used ggplot2 to analyze the accumulation density

p <- ggplot(mydata12, aes(x = intron_length, color=intron_type)) + geom_step(aes(y=..y..),stat="ecdf")

It gives me good lines. Now I want to make a comparison between the lines. My question is what the proper way to get a P value between the 3 lines?
I have tried:

> compare_means(intron_length~intron_type, data = mydata12)

A tibble: 3 x 8

.y. group1 group2 p p.adj p.format p.signif method
<chr> <chr> <chr> <dbl> <dbl> <chr> <chr> <chr>
1 intron_length All_intron All_retained_intron 0. 0. <2e-16 * Wilcoxon 2 intron_length All_intron dynamic_intron 0. 0. <2e-16 * Wilcoxon 3 intron_length All_retained_intron dynamic_intron 1.42e-79 1.40e-79 <2e-16 ** Wilcoxon

> my_comparisons <- list(c("All_intron", "All_retained_intron"), c("All_intron", "dynamic_intron"), c("All_retained_intron", "dynamic_intron"))
> p + stat_compare_means(comparisons = my_comparisons)

Error in f(...) : Can only handle data with groups that are plotted on the x-axis

I have been thinking about getting the slope of the line and make a comparison, is it right and if yes, how can I do it?

Thanks,

R software error • 646 views
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