ez.barplot: barplot with ggplot

In jerryzhujian9/zmisc: ez Zhu's miscellaneous functions

barplot with ggplot

Description

barplot with ggplot

Usage

ez.barplot(
  df,
  cmd,
  color = "color",
  colors = ez.palette("Zhu"),
  bar.gap = 0.7,
  bar.width = 0.7,
  error.size = 0.7,
  error.gap = 0.7,
  error.width = 0.3,
  error.direction = "both",
  ylimits = NULL,
  ybreaks = NULL,
  ylab = NULL,
  xlab = NULL,
  zlab = NULL,
  legend.position = "top",
  legend.direction = "horizontal",
  legend.box = T,
  legend.size = c(0, 10),
  xangle = 0,
  vjust = NULL,
  hjust = NULL,
  print2scr = TRUE,
  point = FALSE,
  point.jitter = 0.15,
  point.size = 1.5,
  point.alpha = 1,
  point.color = "grey55",
  theme.apa = TRUE,
  reorder = FALSE,
  reorder.direction = "az",
  signif = TRUE,
  prefix = -1,
  pe = TRUE,
  showns = FALSE,
  comparisons = NULL,
  annotations = NULL,
  map_signif_level = FALSE,
  y_position = NULL,
  xmin = NULL,
  xmax = NULL,
  margin_top = 0.1,
  step_increase = 0.5,
  extend_line = 0,
  tip_length = 0.15,
  size = 0.5,
  textsize = 3.88,
  family = "",
  vjust2 = 0.4,
  parse = FALSE,
  manual = FALSE,
  orientation = NA,
  na.rm = TRUE,
  ...
)

Arguments

df	data frame in long format (but be careful that standard error might be inaccurate depending on grouping in the long format) if it is already summary data, use mutate(tidyr::uncount(counter), value = 1) to turn into long format
cmd	like "y|x, y|x z, y|x z a", where y (axis) is continous, x (axis) z/a (legend) are discrete; during plot x z a ->x za(combined) or "y|x+covar1+covar2+..." (currently only supports anovas1b with/without covar)
color	"bw" or "color" black/white or colorblind-friendly color
bar.gap	the gap between bars
bar.width	the width of bar itself
error.size	the thickness of error bar (vertical and horizontal lines)
error.gap	the location of errorbar, should be equal to bar.width(?)
error.width	the width of error bar (horizontal lines), could be 0 to show only vertical lines
error.direction	"both", "max", "min"
ylimits	or ylim, e.g.,c(0,0.5). ylimits does not require ybreaks set
ybreaks	e.g.,seq(0,0.5,by=0.1). ybreaks requires ylimits set
ylab	y label NULL
xlab	x label NULL
zlab	z/a/fill/legend label, only applicable when there is z provided NULL
legend.position	legend position 'top', 'bottom', 'left', 'right', 'none', c(x,y,two-element numeric vector) c(0,0) corresponds to the "bottom left" and c(1,1) corresponds to the "top right" position. if no z/a (legend) provided, auto force to 'none'
legend.direction	horizontal or vertical
legend.box	box of legend, T or F
legend.size	c(0,10) the first number 0 controls the legend title, 0=hide; the second number controls legend.key.size, legend.text
xangle	angle of x text 0
vjust	vjust of x text NULL
hjust	hjust of x text NULL
reorder	T/F whether to reorder x by the group means (raw means if no covar, adjusted means if covar)
reorder.direction	'az' or 'za'
signif	add signif to the plot (only works for anovas1b with/without covar)
prefix	-1 (****,***,**,*,ns); 0 (< .0001, < .001, .003, .2); 1 (< .0001, < .001, = .003, = .02); 2 (p < .0001, < .001, p = .003, p = .02)
pe	affects only p < .0001 or < .001. if T, would be sth like 3.14e-04; otherwise < .0001 or < .001
showns	if T, show ns or .2; F, only display significant ones
comparisons	A list of length-2 vectors. The entries in the vector are either the names of 2 values on the x-axis or the 2 integers that correspond to the index of the columns of interest. if NULL, permute all combinations. e.g., comparisons = list(c("compact", "pickup"), c("subcompact", "suv"))
annotations	character vector with alternative annotations. if NULL, auto compute annotations = c("First", "Second"), formatC(0.92, digits=1)
map_signif_level	NOT WORKING (because I manually pass in annotations?)–Use prefix=-1, Boolean value, if the p-value are directly written as annotation or asterisks are used instead. Alternatively one can provide a named numeric vector to create custom mappings from p-values to annotation: For example: 'c("***"=0.001, "**"=0.01, "*"=0.05)'. Alternatively, one can provide a function that takes a numeric argument (the p-value) and returns a string. map_signif_level = function(p) sprintf("p = %.2g", p)
y_position	numeric vector with the y positions of the brackets
xmin, xmax	numeric vector with the positions of the left and right sides of the brackets, respectively
margin_top	controls distance between the bar and the line. numeric vector how much higher that the maximum value that bars start as fraction of total height
step_increase	numeric vector with the increase in fraction of total height for every additional comparison to minimize overlap.
extend_line	Numeric that allows to shorten (negative values) or extend (positive value) the horizontal line between groups for each comparison; defaults to 0. bar goes down to indicate the precise column
tip_length	numeric vector with the fraction of total height that the
size	change the thickness of the lines of the bracket
textsize	change the size of the text
family	change the font used for the text
vjust2	move the text up or down relative to the bracket (+down,-up)
parse	If 'TRUE', the labels will be parsed into expressions and displayed as described in '?plotmath'.
manual	Boolean flag that indicates that the parameters are provided with a data.frame. This option is necessary if one wants to plot different annotations per facet.
orientation	The orientation of the layer. The default ('NA') automatically determines the orientation from the aesthetic mapping. In the rare event that this fails it can be given explicitly by setting 'orientation' to either "x" or "y"
na.rm	If 'FALSE', removes missing values with a warning. If 'TRUE' silently removes missing values.
...	additional params to geom_signif

Value

a ggplot object (+theme_apa() to get apa format plot), +scale_y_continuous(limits=c(-5,8),breaks=seq(-5,8,by=2),oob=scales::rescale_none)
see http://stackoverflow.com/a/31437048/2292993 for discussion

jerryzhujian9/zmisc documentation built on Sept. 24, 2024, 2:40 p.m.