get_pvalue_position: Autocompute P-value Positions For Plotting Significance

In kassambara/rstatix: Pipe-Friendly Framework for Basic Statistical Tests

Autocompute P-value Positions For Plotting Significance

Description

Compute p-value x and y positions for plotting significance levels. Many examples are provided at :

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

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

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

Usage

get_y_position(
  data,
  formula,
  fun = "max",
  ref.group = NULL,
  comparisons = NULL,
  step.increase = 0.12,
  y.trans = NULL,
  stack = FALSE,
  scales = c("fixed", "free", "free_y")
)

add_y_position(
  test,
  fun = "max",
  step.increase = 0.12,
  data = NULL,
  formula = NULL,
  ref.group = NULL,
  comparisons = NULL,
  y.trans = NULL,
  stack = FALSE,
  scales = c("fixed", "free", "free_y")
)

add_x_position(test, x = NULL, group = NULL, dodge = 0.8)

add_xy_position(
  test,
  x = NULL,
  group = NULL,
  dodge = 0.8,
  stack = FALSE,
  fun = "max",
  step.increase = 0.12,
  scales = c("fixed", "free", "free_y"),
  ...
)

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 functions used to compute automatically suitable y positions of p-value labels and brackets. Possible values include: "max", "mean", "mean_sd", "mean_se", "mean_ci", "median", "median_iqr", "median_mad". For example, if fun = "max", the y positions are guessed as follow: 1. Compute the maximum of each group (groups.maximum) 2. Use the highest groups maximum as the first bracket y position 3. Add successively a step increase for remaining bracket y positions. When the main plot is a boxplot, you need the option fun = "max", to have the p-value bracket displayed at the maximum point of the group. In some situations the main plot is a line plot or a barplot showing the mean+/-error bars of the groups, where error can be SE (standard error), SD (standard deviation) or CI (confidence interval). In this case, to correctly compute the bracket y position you need the option fun = "mean_se", etc.
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.
y.trans	a function for transforming y axis scale. Value can be log2, log10 and sqrt. Can be also any custom function that can take a numeric vector as input and returns a numeric vector, example: y.trans = function(x){log2(x+1)}
stack	logical. If TRUE, computes y position for a stacked plot. Useful when dealing with stacked bar plots.
scales	Should scales be fixed ("fixed", the default), free ("free"), or free in one dimension ("free_y")?. This option is considered only when determining the y position. If the specified value is "free" or "free_y", then the step increase of y positions will be calculated by plot panels. Note that, using "free" or "free_y" gives the same result. A global step increase is computed when scales = "fixed".
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.
group	group variable (legend variable).
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

# 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()

 if(require("ggpubr")){
   ggboxplot(df, x = "dose", y = "len") +
     stat_pvalue_manual(stat.test, label = "p.adj.signif", tip.length = 0.01)
  }

kassambara/rstatix documentation built on Feb. 6, 2023, 3:36 a.m.