Bar plot — Bior_BarPlot • Biorplot

Create a stacked barplot.

Bior_BarPlot(
  data,
  x,
  y,
  combine = FALSE,
  merge = FALSE,
  color = "black",
  fill = "white",
  palette = NULL,
  size = NULL,
  width = NULL,
  title = NULL,
  xlab = NULL,
  ylab = NULL,
  facet.by = NULL,
  panel.labs = NULL,
  short.panel.labs = TRUE,
  select = NULL,
  remove = NULL,
  order = NULL,
  add = "none",
  add.params = list(),
  error.plot = "errorbar",
  label = FALSE,
  lab.col = "black",
  lab.size = 4,
  lab.pos = c("out", "in"),
  lab.vjust = NULL,
  lab.hjust = NULL,
  lab.nb.digits = NULL,
  sort.val = c("none", "desc", "asc"),
  sort.by.groups = TRUE,
  top = Inf,
  position = position_stack(),
  ggtheme = theme_pubr(),
  ...
)

Arguments

data

a data frame

x, y

x and y variables for drawing.

combine

logical value. Default is FALSE. Used only when y is a vector containing multiple variables to plot. If TRUE, create a multi-panel plot by combining the plot of y variables.

merge

logical or character value. Default is FALSE. Used only when y is a vector containing multiple variables to plot. If TRUE, merge multiple y variables in the same plotting area. Allowed values include also "asis" (TRUE) and "flip". If merge = "flip", then y variables are used as x tick labels and the x variable is used as grouping variable.

color, fill

outline and fill colors.

palette

the color palette to be used for coloring or filling by groups. Allowed values include "grey" for grey color palettes; brewer palettes e.g. "RdBu", "Blues", ...; or custom color palette e.g. c("blue", "red"); and scientific journal palettes from ggsci R package, e.g.: "npg", "aaas", "lancet", "jco", "ucscgb", "uchicago", "simpsons" and "rickandmorty".

size

Numeric value (e.g.: size = 1). change the size of points and outlines.

width

numeric value between 0 and 1 specifying box width.

title

plot main title.

xlab

character vector specifying x axis labels. Use xlab = FALSE to hide xlab.

ylab

character vector specifying y axis labels. Use ylab = FALSE to hide ylab.

facet.by

character vector, of length 1 or 2, specifying grouping variables for faceting the plot into multiple panels. Should be in the data.

panel.labs

a list of one or two character vectors to modify facet panel labels. For example, panel.labs = list(sex = c("Male", "Female")) specifies the labels for the "sex" variable. For two grouping variables, you can use for example panel.labs = list(sex = c("Male", "Female"), rx = c("Obs", "Lev", "Lev2") ).

short.panel.labs

logical value. Default is TRUE. If TRUE, create short labels for panels by omitting variable names; in other words panels will be labelled only by variable grouping levels.

select

character vector specifying which items to display.

remove

character vector specifying which items to remove from the plot.

order

character vector specifying the order of items.

add

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.

add.params

parameters (color, shape, size, fill, linetype) for the argument 'add'; e.g.: add.params = list(color = "red").

error.plot

plot type used to visualize error. Allowed values are one of c("pointrange", "linerange", "crossbar", "errorbar", "upper_errorbar", "lower_errorbar", "upper_pointrange", "lower_pointrange", "upper_linerange", "lower_linerange"). Default value is "pointrange" or "errorbar". Used only when add != "none" and add contains one "mean_*" or "med_*" where "*" = sd, se, ....

label

specify whether to add labels on the bar plot. Allowed values are:

logical value: If TRUE, y values is added as labels on the bar plot
character vector: Used as text labels; must be the same length as y.

lab.col, lab.size

text color and size for labels.

lab.pos

character specifying the position for labels. Allowed values are "out" (for outside) or "in" (for inside). Ignored when lab.vjust != NULL.

lab.vjust

numeric, vertical justification of labels. Provide negative value (e.g.: -0.4) to put labels outside the bars or positive value to put labels inside (e.g.: 2).

lab.hjust

numeric, horizontal justification of labels.

lab.nb.digits

integer indicating the number of decimal places (round) to be used.

sort.val

a string specifying whether the value should be sorted. Allowed values are "none" (no sorting), "asc" (for ascending) or "desc" (for descending).

sort.by.groups

logical value. If TRUE the data are sorted by groups. Used only when sort.val != "none".

top

a numeric value specifying the number of top elements to be shown.

position

Position adjustment, either as a string naming the adjustment (e.g. "jitter" to use position_jitter), or the result of a call to a position adjustment function. Use the latter if you need to change the settings of the adjustment.

ggtheme

function, ggplot2 theme name. Default value is theme_pubr(). Allowed values include ggplot2 official themes: theme_gray(), theme_bw(), theme_minimal(), theme_classic(), theme_void(), ....

...

other arguments to be passed to be passed to ggpar().

Value

A ggplot object

Examples

# Examples 1
df <- data.frame(
x = c("A", "B", "C"),
y = c(3, 2, 1))
Bior_BarPlot(df, "x", "y", fill = "steelblue", color = "steelblue")


# Examples 2
df <- data.frame(
  x = rep(c('sample1','sample2','sample3','sample4'), each=2),
  y = c(20,16,29,16,14,11,22,21),
  type = rep(c('gene1','gene2'), 4),
  label = c(20,16,29,16,14,11,"","")
  )
col <- c("#AEC7E8FF","#FFBB78FF")
Bior_BarPlot(df, "x", "y", fill = "type", color = "type", label = df$label,
             palette = col, lab.pos = "in") +
  theme(legend.position = "right", legend.key.size=unit(1, "cm"))


# Examples 3
Bior_BarPlot(df, "x", "y", fill = "type", color = "type", palette = col,
             label = TRUE, position = position_dodge(0.9))