plotJitterBoxplot: Boxplot with jitter, barplot with mean_se, violin plot with...

In ProfessionalFarmer/loonR: Common function in bioinformatics analysis

Boxplot with jitter, barplot with mean_se, violin plot with box

Description

Boxplot with jitter, barplot with mean_se, violin plot with box

Usage

plotJitterBoxplot(
  xvalues,
  yvalues,
  group,
  title = "",
  xlab = "",
  ylab = "Value",
  group.name = "Group",
  color = "aaas",
  color.by.x = FALSE,
  comparisons = NULL,
  method = "wilcox.test",
  label.y = NULL,
  add = NULL,
  alternative = "two.sided",
  rotate.x = 0,
  outlier.shape = 19,
  ylim = NULL,
  stat = FALSE,
  barplot = FALSE,
  violin = FALSE,
  facet = FALSE,
  dotplot = FALSE,
  shape.color.by = "black",
  fill.color.by = NULL,
  legend.pos = "",
  scales = "fixed",
  group.position = ggplot2::position_dodge(0.9),
  remove.element = NULL,
  element_text_size = 14,
  facet.n.row = 1
)

Arguments

group	vector
group.name	Default "Group"
color.by.x	Group by x lab. In this way we can perform stats
comparisons	list( c("N", "T") )
method	wilcox.test or t.test
add	Default jitter for boxplot, mean_se for barplot, boxplot for violin and dot plot. character vector for adding another plot element (e.g.: dot plot or error bars). Allowed values are one or the combination of: "none", "dotplot", "jitter", "boxplot", "point", "mean", "mean_se", "mean_sd", "mean_ci", "mean_range", "median", "median_iqr", "median_hilow", "median_q1q3", "median_mad", "median_range"; see ?desc_statby for more details.
alternative	should be one of “two.sided”, “less”, “greater”
rotate.x	Default 0. numeric value specifying the rotation angle. 90 for vertical x-axis text.
outlier.shape	point shape of outlier. Default is 19. To hide outlier, specify outlier.shape = NA. When jitter is added, then outliers will be automatically hidden.
stat	Default FALSE
facet	stat can work only after setting facet=TRUE
shape.color.by	Default "black". If you want set the color by group, please set the group name (Default "Group"). Shape color by group
fill.color.by	Default by "Group". If you want set the color by group, please set the group name (Default "Group"). Shape color by group
legend.pos	one of c("", "top", "bottom", "left", "right", "none")
scales	fixed or free
group.position	Allowed values include "identity", "stack", "dodge", "position_dodge(0.9)", position_stack(). Position adjustment, either as a string, or the result of a call to a position adjustment function
remove.element	Please refer https://rpkgs.datanovia.com/ggpubr/reference/rremove.html
element_text_size	Facet title text size

Examples

data("LIRI")

d.frame = LIRI[,3:6]
group = LIRI$status
liri.melt <- loonR::meltDataFrameByGroup(d.frame, group)

xvalues=liri.melt$Gene
yvalues=liri.melt$value
group=liri.melt$Group

loonR::plotJitterBoxplot(xvalues, yvalues, group, violin = T, facet = T)

ProfessionalFarmer/loonR documentation built on Oct. 9, 2024, 9:56 p.m.