Add Manually P-values to a ggplot — stat_pvalue_manual (2024)

Source: R/stat_pvalue_manual.R

stat_pvalue_manual.Rd

Add manually p-values to a ggplot, such as box blots, dot plots and stripcharts. Frequently asked questions are available on Datanovia ggpubr FAQ page, for example:

• How to Add P-Values onto Basic GGPLOTS

• How to Add Adjusted P-values to a Multi-Panel GGPlot

• How to Add P-values to GGPLOT Facets

• How to Add P-Values Generated Elsewhere to a GGPLOT

• How to Add P-Values onto a Grouped GGPLOT using the GGPUBR R Package

  See Also

  Coordinate System - Scratch WikiPositioning - Learn web development | MDN

• How to Create Stacked Bar Plots with Error Bars and P-values

• How to Add P-Values onto Horizontal GGPLOTS

Arguments

data

a data frame containing statitistical test results. The expecteddefault format should contain the following columns: group1 | group2 |p | y.position | etc. group1 and group2 are the groups thathave been compared. p is the resulting p-value. y.position isthe y coordinates of the p-values in the plot.

label

the column containing the label (e.g.: label = "p" or label ="p.adj"), where p is the p-value. Can be also an expression that canbe formatted by the glue() package. For example, whenspecifying label = "t-test, p = {p}", the expression {p} will bereplaced by its value.

y.position

column containing the coordinates (in data units) to be usedfor absolute positioning of the label. Default value is "y.position". Can bealso a numeric vector.

xmin

column containing the position of the left sides of the brackets.Default value is "group1".

xmax

(optional) column containing the position of the right sides ofthe brackets. Default value is "group2". If NULL, the p-values are plottedas a simple text.

x

x position of the p-value. Should be used only when you want plot thep-value as text (without brackets).

size, label.size

size of label text.

bracket.size

Width of the lines of the bracket.

bracket.nudge.y

Vertical adjustment to nudge brackets by. Useful tomove up or move down the bracket. If positive value, brackets will be movedup; if negative value, brackets are moved down.

bracket.shorten

a small numeric value in [0-1] for shortening the withof bracket.

color

text and line color. Can be variable name in the data for coloring by groups.

linetype

linetype. Can be variable name in the data for changing linetype by groups.

tip.length

numeric vector with the fraction of total height that thebar goes down to indicate the precise column. Default is 0.03.

remove.bracket

logical, if TRUE, brackets are removed from theplot. Considered only in the situation, where comparisons are performedagainst reference group or against "all".

step.increase

numeric vector with the increase in fraction of totalheight for every additional comparison to minimize overlap.

step.group.by

a variable name for grouping brackets before addingstep.increase. Useful to group bracket by facet panel.

hide.ns

can be logical value or a character vector.

• Case when logical value. If TRUE, hide ns symbol when displaying significance levels. Filter is done by checking the column p.adj.signif, p.signif, p.adj and p.

• Case when character value. Possible values are "p" or "p.adj", for filtering out non significant.

vjust

move the text up or down relative to the bracket. Can be also acolumn name available in the data.

coord.flip

logical. If TRUE, flip x and y coordinates so thathorizontal becomes vertical, and vertical, horizontal. When adding thep-values to a horizontal ggplot (generated usingcoord_flip()), you need to specify the optioncoord.flip = TRUE.

position

position adjustment, either as a string, or the result of acall to a position adjustment function.

...

other arguments passed to the function geom_bracket() orgeom_text()

See also

Examples

# T-teststat.test <- compare_means( len ~ dose, data = ToothGrowth, method = "t.test")stat.test#> # A tibble: 3 × 8#> .y. group1 group2 p p.adj p.format p.signif method#> <chr> <chr> <chr> <dbl> <dbl> <chr> <chr> <chr> #> 1 len 0.5 1 1.27e- 7 2.5e- 7 1.3e-07 **** T-test#> 2 len 0.5 2 4.40e-14 1.3e-13 4.4e-14 **** T-test#> 3 len 1 2 1.91e- 5 1.9e- 5 1.9e-05 **** T-test# Create a simple box plotp <- ggboxplot(ToothGrowth, x = "dose", y = "len")p# Perform a t-test between groupsstat.test <- compare_means( len ~ dose, data = ToothGrowth, method = "t.test")stat.test#> # A tibble: 3 × 8#> .y. group1 group2 p p.adj p.format p.signif method#> <chr> <chr> <chr> <dbl> <dbl> <chr> <chr> <chr> #> 1 len 0.5 1 1.27e- 7 2.5e- 7 1.3e-07 **** T-test#> 2 len 0.5 2 4.40e-14 1.3e-13 4.4e-14 **** T-test#> 3 len 1 2 1.91e- 5 1.9e- 5 1.9e-05 **** T-test# Add manually p-values from stat.test data# First specify the y.position of each comparisonstat.test <- stat.test %>% mutate(y.position = c(29, 35, 39))p + stat_pvalue_manual(stat.test, label = "p.adj")# Customize the label with glue expression# (https://github.com/tidyverse/glue)p + stat_pvalue_manual(stat.test, label = "p = {p.adj}")# Grouped bar plots#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%ToothGrowth$dose <- as.factor(ToothGrowth$dose)# Comparisons against referencestat.test <- compare_means( len ~ dose, data = ToothGrowth, group.by = "supp", method = "t.test", ref.group = "0.5")stat.test#> # A tibble: 4 × 9#> supp .y. group1 group2 p p.adj p.format p.signif method#> <fct> <chr> <chr> <chr> <dbl> <dbl> <chr> <chr> <chr> #> 1 VC len 0.5 1 0.000000681 0.000002 6.8e-07 **** T-test#> 2 VC len 0.5 2 0.0000000468 0.00000019 4.7e-08 **** T-test#> 3 OJ len 0.5 1 0.0000878 0.000088 8.8e-05 **** T-test#> 4 OJ len 0.5 2 0.00000132 0.0000026 1.3e-06 **** T-test# Plotbp <- ggbarplot(ToothGrowth, x = "supp", y = "len", fill = "dose", palette = "jco", add = "mean_sd", add.params = list(group = "dose"), position = position_dodge(0.8))bp + stat_pvalue_manual( stat.test, x = "supp", y.position = 33, label = "p.signif", position = position_dodge(0.8))