Description

visBoxplotAdv is supposed to visualise a data frame using advanced boxplot. In addition to boxplot, a scatter plot is also drawn with various methods to avoid co-incident points so that each point is visible (with fine-controling the color and plotting character). Also, these points can be pies or thermometers, which allows an additional proportation data to be visualised as well.

Usage

visBoxplotAdv(formula, data, orientation = c("vertical", "horizontal"), method = c("center", 
  "hex", "square", "swarm"), corral = c("none", "gutter", "wrap", "random", "omit"), 
      corralWidth, cex = 1, spacing = 1, breaks = NULL, labels, at = NULL, add = FALSE, 
      log = FALSE, xlim = NULL, ylim = NULL, xlab = NULL, ylab = NULL, pch = c("circles", 
          "thermometers", "pies")[1], col = graphics::par("col"), bg = NA, pwpch = NULL, 
      pwcol = NULL, pwbg = NULL, pwpie = NULL, do.plot = TRUE, do.boxplot = TRUE, boxplot.notch = FALSE, 
      boxplot.border = "#888888C0", boxplot.col = "transparent", ...)

Arguments

formula

a formula, such as 'y ~ grp', where 'y' is a numeric vector of data values to be split into groups according to the grouping variable 'grp' (usually a factor)

data

a data.frame (or list) from which the variables in 'formula' should be taken.

orientation

the orientation. It can be one of "vertical" for the vertical orientation, "horizontal" for the horizontal orientation

method

the method for arranging the points. It can be one of "swarm" for arranging points in increasing order (if a point would overlap an existing point, it is shifted sideways (along the group axis) by a minimal amount sufficient to avoid overlap), "center" for first discretizing the values along the data axis (in order to create more efficient packing) and then using a square grid to produce a symmetric swarm, "hex" for first discretization and then arranging points in a hexagonal grid, and "square" for first discretization and then arranging points in a square grid

corral

the method to adjust points that would be placed outside their own group region. It can be one of "none" for not adjusting runaway points, "gutter" for collecting runaway points along the boundary between groups, "wrap" for wrapping runaway points to produce periodic boundaries, "random" for placing runaway points randomly in the region, and "omit" for omitting runaway points

corralWidth

the width of the "corral" in user coordinates

cex

size of points relative to the default. This must be a single value

spacing

relative spacing between points

breaks

breakpoints (optional). If NULL, breakpoints are chosen automatically

labels

labels for each group. Recycled if necessary. By default, these are inferred from the data

at

numeric vector giving the locations where the swarms should be drawn; defaults to '1:n' where n is the number of groups

add

whether to add to an existing plot

log

whether to use a logarithmic scale on the data axis

xlim

limits for x-axis

ylim

limits for y-axis

xlab

labels for x-aixs

ylab

labels for y-aixs

pch

plotting characters, specified by group and recycled if necessary. In additon to the convertional pch values, it can also be "circles", "thermometers", or "pies". For "pies" (or "thermometers"), users can also specify the proportional values (see below "pwpie") to visualise another information in the pie (or themometer) chart

col

plotting colors, specified by group and recycled if necessary

bg

plotting background, specified by group and recycled if necessary

pwpch

point-wise version of pch

pwcol

point-wise version of col

pwbg

point-wise version of bg

pwpie

point-wise proportion used when drawing pies or themometers

do.plot

whether to draw main plot

do.boxplot

whether to draw boxplot. It only works when the main plot is drawn

boxplot.notch

whether to draw a notch in the boxplot. If the notches of two plots do not overlap this is 'strong evidence' that the two medians differ

boxplot.border

the color for the outlines of the boxplots

boxplot.col

the color for the bodies of the boxplots

...

additional graphic parameters for the plot

Value

A data frame with plotting information. It has the same row names as the input data

Note

none

Examples

data(TCGA_mutations)
pd <- Biobase::pData(TCGA_mutations)
# only tumor types "LAML" or "BLCA"
data <- pd[pd$TCGA_tumor_type=="LAML" | pd$TCGA_tumor_type=="BLCA",]
labels <- levels(as.factor(data$TCGA_tumor_type))
# colors for gender
pwcol <- as.numeric((data$Gender))
# pie for relative age
pwpie <- data$Age/(max(data$Age))
out <- visBoxplotAdv(formula=time ~ TCGA_tumor_type, data=data,
pch="pies", pwcol=pwcol, pwpie=pwpie)


legend("topright", legend=levels(data$Gender), box.col="transparent",
pch=19, col=unique(pwcol))

Source code

Source man

See also