niceBar: draw a bar plot

In ZachHunter/NicePlots.R: Nice Plots for Data Exploration

draw a bar plot

Description

Aggregates data from a numeric vector or dataframe using up to three factors to draw a barplot with optional error bars.

Usage

niceBar(
  x,
  by = NULL,
  groupLabels = NULL,
  aggFun = c("mean", "median", "none"),
  errFun = c("sd", "se", "range"),
  theme = basicTheme,
  legend = FALSE,
  stack = FALSE,
  main = NULL,
  sub = NULL,
  ylab = NULL,
  minorTick = FALSE,
  guides = TRUE,
  outliers = FALSE,
  width = NULL,
  errorMultiple = 2,
  plotColors = list(bg = "open", fill = setAlpha("grey", 0.8)),
  logScale = FALSE,
  trim = FALSE,
  axisText = c(NULL, NULL),
  showCalc = FALSE,
  calcType = "wilcox",
  yLim = NULL,
  rotateLabels = FALSE,
  rotateY = TRUE,
  add = FALSE,
  minorGuides = NULL,
  extendTicks = TRUE,
  subgroup = FALSE,
  subgroupLabels = NULL,
  stackLabels = NULL,
  expLabels = FALSE,
  sidePlot = FALSE,
  errorBars = TRUE,
  errorCap = "ball",
  errorLineType = 1,
  capWidth = 1.2,
  lWidth = 1.5,
  na.rm = FALSE,
  flipFacts = FALSE,
  verbose = FALSE,
  logAdjustment = 1,
  normalize = FALSE,
  ...
)

Arguments

x	numeric vector or data frame; The input to prepCategoryWindow can be a numeric vector a data frame of numeric vectors.
by	factor or data frame of factors; used as the primary grouping factor and the factor levels will be used as group names if groupLabels is not specified. If by is a data frame and subgroup=TRUE, the second column is assumed to be a secondary grouping factor, breaking out the data into sub-categories within each major group determined by the levels of the first column.
groupLabels	character vector; overrides the factor levels of by to label the groups
aggFun	character; Determines how the data is summarized by factor level. Valid options are mean, median or none.
errFun	character; How the data spread is charactarized by the error bars. Valid options are sd (standard deviation), se (standard error of the mean, range, t95ci (t-distributoin 95% CI), or boot95ci (empirical bootstrap 95%ci).
theme	list object; Themes are are an optional way of storing graphical preset options that are compatible with all nicePlot graphing functions.
legend	logical/character; if not equal to FALSE with cause a legend to be drawn in the margins. If set to a character string instead of a logical value, the string will be used as the legend title insteas of the factor column name from by.
stack	logical; Should one of the factors in by be used make a stacked bar plot. Note that this sort of analysis is nonsensical for many data sets.
main	character; title for the graph which is supplied to the main argument.
sub	character; subtitle for the graph which is supplied to the sub argument. If NULL and showCalc=TRUE it will be used to display the output form calcStats.
ylab	character; y-axis label.
minorTick	positive integer; number of minor tick-marks to draw between each pair of major ticks-marks.
guides	logical; will draw guidelines at the major tick-marks if set to TRUE. Color of the guidelines is determined by plotColors$guides.
outliers	positive numeric; number of interquartile ranges (IQR) past the Q1 (25%) and Q3 (75%) cumulative distribution values. Outliers are often defined as 1.5 \times IQR and extreme outliers are more than 3 \times IQR away from the inner 50% data range.
width	numeric; cex-like scaling factor controlling the width of the bars.
errorMultiple	numeric; How many standard errors/deviations should be represented by the error bars.
plotColors	list; a named list of vectors of colors that set the color options for all NicePlot functions. Names left unspecified will be added and set to default values automatically.
logScale	positive numeric; the base for the for log scale data transformation calculated as log(x+1,logScale).
trim	positive numeric; passed to threshold argument of quantileTrim if any data points are so extreme that they should be removed before plotting and downstream analysis. Set to FALSE to disable.
axisText	character; a length two character vector containing text to be prepended or appended to the major tick labels, respectively.
showCalc	logical; if a p-value can be easily calculated for your data, it will be displayed using the sub annotation setting.
calcType	character; should match one of 'none', 'wilcox', 'Tukey','t.test','anova' which will determine which, if any statistical test should be performed on the data.
yLim	numeric vector; manually set the limits of the plotting area (eg. yLim=c(min,max)). Used to format the y-axis by default but will modify the x-axis if side=TRUE.
rotateLabels	logical; sets las=2 for the x-axis category labels. Will affect y-axis if side=TRUE. Note that this may not work well if long names or with subgrouped data.
rotateY	logical; sets las=2 for the y-axis major tick-mark labels. Will affect x-axis if side=TRUE.
add	logical; causes plotting to be added to the existing plot rather the start a new one.
minorGuides	logical; draws guidelines at minor tick-marks
extendTicks	logical; extends minor tick-marks past the first and last major tick to the edge of the graph provided there is enough room. Works for both log-scale and regular settings.
subgroup	logical; use additional column in by to group the data within each level of the major factor.
subgroupLabels	character vector; sets the labels used for the subgroup factor. Defaults to the levels of the factor.
stackLabels	character; An optional character vector to override the factor labels associated with stacking factor if active.
expLabels	logical; prints the major tick labels is logScale^{x} instead of the raw value
sidePlot	logical; switches the axis to plot horizontally instead of vertically.
errorBars	Logical; Should error bars be drawn. Defaults to true but is ignored if stack=TRUE.
errorCap	character; Determines the style for the ends of the error bars. Valid options are ball, bar or none.
errorLineType	numeric; Sets lty line type for drawing the error bars.
capWidth	numeric; Controls the cex like scaling of the ball or width of the cap if they are drawn at the end of the error bars for the bar plot.
lWidth	numeric; Line width (lwd) for drawing the bar plot.
na.rm	logical; Should NAs be removed from the data set? Both data input and the factor input from by with be checked.
flipFacts	logical; When a data.frame of values is given, column names are used as a secondary grouping factor by default. Setting flipFacts=TRUE makes the column names the primary factor and by the secondary factor.
verbose	logical; Prints summary and p-value calculations to the screen. All data is silently by the function returned either way.
logAdjustment	= numeric; This number is added to the input data prior to log transformation. Default value is 1.
normalize	logical; Normalizes stacked bars to 100%. If stacked==TRUE and normalize==TRUE the stacked bars will all go to 100%. Otherwise the bars represent the cumuative value.
...	additional options for S3 method variants.

Details

This bar plot function allows for standard barplot features but with error bars, the ability summaryize dataframes into bar plots with median/mean values, sort by bar hight for waterfall plots, color bars based on interquartile outlier detection and more. Barplots can be clustered by a secondary factor or if a dataframe is passed to x the input values of multiple measurments (dataframe columns) can be clustered together by the primary factor. As with niceBox, niceDots and niceVio, by can be a factor or a dataframe factors for forming subgroups.

For most data this would be nonsensical but if you data is say store profits by goods by region one could group by region (first)

See Also

vioplot, boxplot, niceBox, beeswarm, prepCategoryWindow

Examples

data(mtcars)
Groups<-data.frame(Cyl=factor(mtcars$cyl),Gear=factor(mtcars$gear))
niceBar(mtcars$mpg,by=Groups,subgroup=TRUE,yLim=c(0,45),main="MpG by Cylinders and Gear")

ZachHunter/NicePlots.R documentation built on Sept. 23, 2023, 4:04 a.m.