rstatix (version 0.1.1)

get_y_position: Autocompute P-value Positions For Plotting Significance

Description

Compute p-value x and y positions for plotting significance levels.

Usage

get_y_position(data, formula, fun = "max", ref.group = NULL,
  comparisons = NULL, step.increase = 0.12)
add_y_position(test, fun = "max", step.increase = 0.12, data = NULL,
  formula = NULL, ref.group = NULL, comparisons = NULL)
add_x_position(test, x = NULL, dodge = 0.8)
add_xy_position(test, x = NULL, dodge = 0.8, fun = "max",
  step.increase = 0.12, ...)

Arguments

data

a data.frame containing the variables in the formula.

formula

a formula of the form x ~ group where x is a numeric variable giving the data values and group is a factor with one or multiple levels giving the corresponding groups. For example, formula = TP53 ~ cancer_group.

fun

summary statistics function. Possible values include: "max", "mean", "mean_sd", "mean_se", "mean_ci", "median", "median_iqr", "median_mad".

"max" is suitable when you want to add, for example, p-value on box plots. The remaining functions are suitable for bar plots and line plots showing mean plots +/- error bars.

ref.group

a character string specifying the reference group. If specified, for a given grouping variable, each of the group levels will be compared to the reference group (i.e. control group).

comparisons

A list of length-2 vectors specifying the groups of interest to be compared. For example to compare groups "A" vs "B" and "B" vs "C", the argument is as follow: comparisons = list(c("A", "B"), c("B", "C"))

step.increase

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

test

an object of class rstatix_test as returned by t_test(), wilcox_test(), sign_test(), tukey_hsd(), dunn_test().

x

variable on x axis.

dodge

dodge width for grouped ggplot/test. Default is 0.8. Used only when x specified.

...

other arguments to be passed to the function t.test.

Functions

• get_y_position: compute the p-value y positions

• add_y_position: add p-value y positions to an object of class rstatix_test

• add_x_position: compute and add p-value x positions.

• add_xy_position: compute and add both x and y positions.

Examples

# NOT RUN {
# Data preparation
#::::::::::::::::::::::::::::::::::::
df <- ToothGrowth
df$dose <- as.factor(df$dose)
df$group <- factor(rep(c(1, 2), 30))
head(df)

# Stat tests
#::::::::::::::::::::::::::::::::::::
stat.test <- df %>%
  t_test(len ~ dose)
stat.test

# Add the test into box plots
#::::::::::::::::::::::::::::::::::::
stat.test <- stat.test %>%
  add_y_position()
# }
# NOT RUN {
 if(require("ggpubr")){
   ggboxplot(df, x = "dose", y = "len") +
     stat_pvalue_manual(stat.test, label = "p.adj.signif", tip.length = 0.01)
  }
# }