Make a strip-plot
create.stripplot.RdTakes a formula and a data.frame and creates a strip-plot
Usage
create.stripplot(
formula,
data,
filename = NULL,
groups = NULL,
jitter.data = FALSE,
jitter.factor = 1,
jitter.amount = NULL,
main = NULL,
main.just = 'center',
main.x = 0.5,
main.y = 0.5,
main.cex = 3,
xlab.label = tail(sub('~', '', formula[-2]), 1),
ylab.label = tail(sub('~', '', formula[-3]), 1),
xlab.cex = 2,
ylab.cex = 2,
xlab.col = 'black',
ylab.col = 'black',
xlab.top.label = NULL,
xlab.top.cex = 2,
xlab.top.col = 'black',
xlab.top.just = 'center',
xlab.top.x = 0.5,
xlab.top.y = 0,
xaxis.lab = TRUE,
yaxis.lab = TRUE,
xaxis.cex = 1.5,
yaxis.cex = 1.5,
xaxis.col = 'black',
yaxis.col = 'black',
xaxis.fontface = 'bold',
yaxis.fontface = 'bold',
xaxis.rot = 0,
yaxis.rot = 0,
xaxis.tck = 0,
yaxis.tck = 1,
xlimits = NULL,
ylimits = NULL,
xat = TRUE,
yat = TRUE,
lwd = 1,
pch = 19,
col = 'black',
col.border = 'black',
fill = 'transparent',
colour.alpha = 1,
cex = 0.75,
top.padding = 0.1,
bottom.padding = 0.7,
right.padding = 0.3,
left.padding = 0.5,
ylab.axis.padding = 1,
layout = NULL,
as.table = TRUE,
x.spacing = 0,
y.spacing = 0,
add.median = FALSE,
median.values = NULL,
add.rectangle = FALSE,
xleft.rectangle = NULL,
ybottom.rectangle = NULL,
xright.rectangle = NULL,
ytop.rectangle = NULL,
col.rectangle = 'transparent',
alpha.rectangle = 1,
strip.col = 'white',
strip.cex = 1,
strip.fontface = 'bold',
key = NULL,
legend = NULL,
height = 6,
width = 6,
size.units = 'in',
resolution = 1600,
enable.warnings = FALSE,
description = 'Created with BoutrosLab.plotting.general',
style = 'BoutrosLab',
preload.default = 'custom',
use.legacy.settings = FALSE,
inside.legend.auto = FALSE,
disable.factor.sorting = FALSE
)Arguments
- formula
The formula used to extract the x & y components from the data-frame
- data
The data-frame to plot
- filename
Filename for tiff output, or if NULL returns the trellis object itself
- groups
The grouping variable in the data-frame
- jitter.data
Allow data to be staggered, default is FALSE
- jitter.factor
Numeric value to apply to jitter, default is 1
- jitter.amount
Numeric; amount of noise to add, default is NULL
- main
The main title for the plot (space is reclaimed if NULL)
s
- main.just
The justification of the main title for the plot, default is centered
- main.x
The x location of the main title, deault is 0.5
- main.y
The y location of the main title, default is 0.5
- main.cex
Size of text for main plot title
- xlab.label
X-axis label
- ylab.label
Y-axis label
- xlab.cex
Size of x-axis label, defaults to 3
- ylab.cex
Size of y-axis label, defaults to 3
- xlab.col
Colour of the x-axis label, defaults to “black”
- ylab.col
Colour of the y-axis label, defaults to “black”
- xlab.top.label
The label for the top x-axis
- xlab.top.cex
Size of top x-axis label
- xlab.top.col
Colour of the top x-axis label
- xlab.top.just
Justification of the top x-axis label, defaults to centered
- xlab.top.x
The x location of the top x-axis label
- xlab.top.y
The y location of the top y-axis label
- xaxis.lab
Vector listing x-axis tick labels, defaults to automatic
- yaxis.lab
Vector listing y-axis tick labels, defaults to automatic
- xaxis.cex
Size of x-axis scales, defaults to 2
- yaxis.cex
Size of y-axis scales, defaults to 2
- xaxis.col
Colour of the x-axis tick labels, defaults to “black”
- yaxis.col
Colour of the y-axis tick labels, defaults to “black”
- xaxis.fontface
Fontface for the x-axis scales
- yaxis.fontface
Fontface for the y-axis scales
- xaxis.rot
Rotation of y-axis tick labels; defaults to 0
- yaxis.rot
Rotation of y-axis tick labels; defaults to 0
- xaxis.tck
Specifies the length of the tick marks for x-axis, defaults to 0
- yaxis.tck
Specifies the length of the tick marks for y-axis, defaults to 1
- xlimits
Two-element vector giving the x-axis limits, default is automatic
- ylimits
Two-element vector giving the y-axis limits, default is automatic
- xat
Vector listing where the x-axis labels should be drawn, default is automatic
- yat
Vector listing where the y-axis labels should be drawn, default is automatic
- lwd
Line width, defaults to 1
- pch
The plotting character (defaults to filled circles)
- col
Colour of the plotting character (defaults to black)
- col.border
Colour of border when pch > 21. Defaults to black
- fill
Fill colour of the plotting character if pch set to 21:25 (defaults to transparent)
- colour.alpha
Bias to be added to colour selection (defaults to 1)
- cex
The size of the plotting character
- top.padding
A number specifying the distance to the top margin, defaults to 0.1
- bottom.padding
A number specifying the distance to the bottom margin, defaults to 0.7
- right.padding
A number specifying the distance to the right margin, defaults to 0.3
- left.padding
A number specifying the distance to the left margin, defaults to 0.5
- ylab.axis.padding
A number specifying the distance of ylabel to the y-axis, defaults to 1
- layout
A vector specifying the number of columns, rows (e.g., c(2,1). Default is NULL; see lattice::xyplot for more details
.
- as.table
Specifies panel drawing order, default is TRUE to draw from top left corner, moving right then down. Set to FALSE to draw panels from bottom left corner, moving right then up
- x.spacing
A number specifying the distance between panels along the x-axis, defaults to 0
- y.spacing
A number specifying the distance between panels along the y-axis, defaults to 0
- add.median
TRUE/FALSE indicating whether lines should be drawn at the group medians, default is FALSE
- median.values
A vector of values representing the median of each group, default is NULL
- add.rectangle
Allow a rectangle to be drawn, default is FALSE
- xleft.rectangle
Specifies the left x coordinate of the rectangle to be drawn
- ybottom.rectangle
Specifies the bottom y coordinate of the rectangle to be drawn
- xright.rectangle
Specifies the right x coordinate of the rectangle to be drawn
- ytop.rectangle
Specifies the top y coordinate of the rectangle to be drawn
- col.rectangle
Specifies the colour to fill the rectangle's area
- alpha.rectangle
Specifies the colour bias of the rectangle to be drawn
- strip.col
Strip background colour, defaults to “white”
- strip.cex
Strip title character expansion
- strip.fontface
Strip text fontface, defaults to bold
- key
A list giving the key (legend). The default suppresses drawing
- legend
Add a legend to the plot. Helpful for adding multiple keys and adding keys to the margins of the plot. See xyplot.
- height
Figure height, defaults to 6 inches
- width
Figure width, defaults to 6 inches
- size.units
Figure units, defaults to inches
- resolution
Figure resolution in dpi, defaults to 1600
- enable.warnings
Print warnings if set to TRUE, defaults to FALSE
- description
Short description of image/plot; default NULL
- style
defaults to “BoutrosLab”, also accepts “Nature”, which changes parameters according to Nature formatting requirements
- preload.default
ability to set multiple sets of diffrent defaults depending on publication needs
- use.legacy.settings
boolean to set wheter or not to use legacy mode settings (font)
- inside.legend.auto
boolean specifying whether or not to use the automatic inside legend function
- disable.factor.sorting
Disable barplot auto sorting factors alphabetically/numerically
Value
If filename is NULL then returns the trellis object, otherwise creates a plot and returns a 0/1 success code.
Warning
If this function is called without capturing the return value, or specifying a filename, it may crash while trying to draw the histogram. In particular, if a script that uses such a call of create histogram is called by reading the script in from the command line, it will fail badly, with an error message about unavailable fonts:
Error in grid.Call.graphics("L_text", as.graphicsAnnot(x$label), x$x, )
Invalid font type
Calls: print ... drawDetails.text -> grid.Call.graphics -> .Call.graphics
Examples
set.seed(12345);
simple.data <- data.frame(
x = c(rep(rnorm(50),5)),
y = as.factor(sample(LETTERS[1:5],250,TRUE))
);
create.stripplot(
# filename = tempfile(pattern = 'Stripplot_simple', fileext = '.tiff'),
formula = x ~ y,
data = simple.data,
resolution = 50
);
# load real datasets
stripplot.data <- data.frame(
values = c(t(microarray[1:10, 1:58])),
genes = rep(rownames(microarray)[1:10], each = 58),
sex = patient$sex,
stringsAsFactors = TRUE
);
# Minimal Input using real data
create.stripplot(
# filename = tempfile(pattern = 'Stripplot_Minimal_Input', fileext = '.tiff'),
formula = genes ~ values,
data = stripplot.data,
main = 'Minimal input',
description = 'Stripplot created by BoutrosLab.plotting.general',
resolution = 50
);
# Axes & Labels
create.stripplot(
# filename = tempfile(pattern = 'Stripplot_Axes_Labels', fileext = '.tiff'),
formula = genes ~ values,
data = stripplot.data,
main = 'Axes & labels',
# formatting axes
xlab.label = 'Change in gene expression',
ylab.label = 'Gene',
xlab.cex = 1.5,
ylab.cex = 1.5,
xaxis.cex = 1,
yaxis.cex = 1,
xaxis.fontface = 1,
yaxis.fontface = 1,
xlimits = c(0,13),
xat = seq(0,12,2),
description = 'Stripplot created by BoutrosLab.plotting.general',
resolution = 100
);
# Colour & Legend
create.stripplot(
# filename = tempfile(pattern = 'Stripplot_Colour_Legend', fileext = '.tiff'),
formula = genes ~ values,
data = stripplot.data,
main = 'Colour & legend',
xlab.label = 'Change in gene expression',
ylab.label = 'Gene',
xlab.cex = 1.5,
ylab.cex = 1.5,
xaxis.cex = 1,
yaxis.cex = 1,
xaxis.fontface = 1,
yaxis.fontface = 1,
xlimits = c(0,13),
xat = seq(0,12,2),
# Colour & points adjustment
groups = stripplot.data$sex,
col = c('pink', 'skyblue'),
pch = 19,
colour.alpha = 0.5,
cex = 1,
# Legend
key = list(
space = 'right',
text = list(
lab = levels(stripplot.data$sex),
cex = 1,
col = 'black'
),
points = list(
pch = 19,
col = c('pink','skyblue'),
alpha = 0.5,
cex = 1
),
padding.text = 3
),
description = 'Stripplot created by BoutrosLab.plotting.general',
resolution = 100
);
# \donttest{
# Jitter
create.stripplot(
# filename = tempfile(pattern = 'Stripplot_Jitter', fileext = '.tiff'),
formula = genes ~ values,
data = stripplot.data,
main = 'Low Jitter',
xlab.label = 'Change in gene expression',
ylab.label = 'Gene',
xlab.cex = 1.5,
ylab.cex = 1.5,
xaxis.cex = 1,
yaxis.cex = 1,
xaxis.fontface = 1,
yaxis.fontface = 1,
xlimits = c(0,13),
xat = seq(0,12,2),
groups = stripplot.data$sex,
col = c('pink', 'skyblue'),
pch = 19,
colour.alpha = 0.5,
cex = 1,
key = list(
space = 'right',
text = list(
lab = levels(stripplot.data$sex),
cex = 1,
col = 'black'
),
points = list(
pch = 19,
col = c('pink','skyblue'),
alpha = 0.4,
cex = 1
),
padding.text = 3
),
# Custom jitter
jitter.data = TRUE,
description = 'Stripplot created by BoutrosLab.plotting.general',
resolution = 200
);
# Jitter
create.stripplot(
# filename = tempfile(pattern = 'Stripplot_High_Jitter', fileext = '.tiff'),
formula = genes ~ values,
data = stripplot.data,
main = 'High Jitter',
xlab.label = 'Change in gene expression',
ylab.label = 'Gene',
xlab.cex = 1.5,
ylab.cex = 1.5,
xaxis.cex = 1,
yaxis.cex = 1,
xaxis.fontface = 1,
yaxis.fontface = 1,
xlimits = c(0,13),
xat = seq(0,12,2),
groups = stripplot.data$sex,
col = c('pink', 'skyblue'),
pch = 19,
colour.alpha = 0.5,
cex = 1,
key = list(
space = 'right',
text = list(
lab = levels(stripplot.data$sex),
cex = 1,
col = 'black'
),
points = list(
pch = 19,
col = c('pink','skyblue'),
alpha = 0.4,
cex = 1
),
padding.text = 3
),
# Custom jitter
jitter.data = TRUE,
jitter.factor = 0.5,
jitter.amount = 0.33,
description = 'Stripplot created by BoutrosLab.plotting.general',
resolution = 200
);
# Nature style
create.stripplot(
# filename = tempfile(pattern = 'Stripplot_Nature_style', fileext = '.tiff'),
formula = genes ~ values,
data = stripplot.data,
main = 'Nature style',
xlab.cex = 1.5,
ylab.cex = 1.5,
xaxis.cex = 1,
yaxis.cex = 1,
xaxis.fontface = 1,
yaxis.fontface = 1,
xlimits = c(0,13),
xat = seq(0,12,2),
groups = stripplot.data$sex,
col = c('pink', 'skyblue'),
pch = 19,
colour.alpha = 0.5,
cex = 1,
key = list(
space = 'right',
text = list(
lab = levels(stripplot.data$sex),
cex = 1,
col = 'black'
),
points = list(
pch = 19,
col = c('pink','skyblue'),
alpha = 0.4,
cex = 1
),
padding.text = 3
),
jitter.data = TRUE,
jitter.factor = 0.5,
jitter.amount = 0.33,
# set style to Nature
style = 'Nature',
# demonstrating how to italicize character variables
ylab.label = expression(paste('italicized ', italic('a'))),
# demonstrating how to create en-dashes
xlab.label = expression(paste('en dashs: 1','\u2013', '10'^'\u2013', ''^3)),
description = 'Stripplot created by BoutrosLab.plotting.general',
resolution = 200
);
#> Warning: Setting resolution to 1200 dpi.
#> Warning: Nature also requires italicized single-letter variables and en-dashes
#> for ranges and negatives. See example in documentation for how to do this.
#> Warning: Avoid red-green colour schemes, create TIFF files, do not outline the figure or legend
# }