| create.polygonplot {BoutrosLab.plotting.general} | R Documentation |
Make a polygonplot
Description
Takes a data.frame and creates a polygon
Usage
create.polygonplot(
formula,
data,
filename = NULL,
groups = NULL,
main = NULL,
main.just = 'center',
main.x = 0.5,
main.y = 0.5,
main.cex = 3,
max,
min,
col = 'white',
alpha = 0.5,
border.col = 'black',
strip.col = 'white',
strip.cex = 1,
type = 'p',
cex = 0.75,
pch = 19,
lwd = 1,
lty = 1,
axes.lwd = 1,
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.rot = 0,
yaxis.rot = 0,
xaxis.log = FALSE,
yaxis.log = FALSE,
xaxis.fontface = 'bold',
yaxis.fontface = 'bold',
xaxis.col = 'black',
yaxis.col = 'black',
xaxis.tck = 1,
yaxis.tck = 1,
xlimits = NULL,
ylimits = NULL,
xat = TRUE,
yat = TRUE,
layout = NULL,
as.table = FALSE,
x.spacing = 0,
y.spacing = 0,
x.relation = 'same',
y.relation = 'same',
top.padding = 0.5,
bottom.padding = 2,
right.padding = 1,
left.padding = 2,
ylab.axis.padding = 0,
add.border = FALSE,
add.xy.border = NULL,
add.median = FALSE,
median.lty = 3,
median.lwd = 1.5,
use.loess.border = FALSE,
use.loess.median = FALSE,
median = NULL,
median.col = 'black',
extra.points = NULL,
extra.points.pch = 21,
extra.points.type = 'p',
extra.points.col = 'black',
extra.points.fill = 'white',
extra.points.cex = 1,
add.rectangle = FALSE,
xleft.rectangle = NULL,
ybottom.rectangle = NULL,
xright.rectangle = NULL,
ytop.rectangle = NULL,
col.rectangle = 'transparent',
alpha.rectangle = 1,
xgrid.at = xat,
ygrid.at = yat,
grid.lty = 1,
grid.col = 'grey',
grid.lwd = 0.3,
add.xyline = FALSE,
xyline.col = 'black',
xyline.lwd = 1,
xyline.lty = 1,
abline.h = NULL,
abline.v = NULL,
abline.col = 'black',
abline.lwd = 1,
abline.lty = 1,
add.text = FALSE,
text.labels = NULL,
text.x = NULL,
text.y = NULL,
text.col = 'black',
text.cex = 1,
text.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
);
Arguments
formula |
The formula used to extract the boxplot 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 |
main |
The main title for the plot (space is reclaimed if NULL) |
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 |
max |
Max values for polygon |
min |
Min values for polygon |
col |
Fill colour of polygon, defaults to white |
alpha |
Transparency of polygons when several are plotted, defaults to 0.5. |
border.col |
Border colour(s) of polygon(s), defaults to black |
strip.col |
Strip background colour, defaults to “white” |
strip.cex |
Strip title character expansion |
type |
Plot type |
cex |
Character expansion for plotting symbol |
pch |
Plotting character |
lwd |
Specifies line width, defaults to 1 |
lty |
Specifies line style, defaults to 1 (solid) |
axes.lwd |
Thickness of width of axes lines |
xlab.label |
The label for the x-axis |
ylab.label |
The label for the y-axis |
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.rot |
Rotation of x-axis tick labels; defaults to 0 |
yaxis.rot |
Rotation of y-axis tick labels; defaults to 0 |
xaxis.log |
Logical indicating whether x-variable should be in logarithmic scale (and what base if numeric) |
yaxis.log |
Logical indicating whether y-variable should be in logarithmic scale (and what base if numeric) |
xaxis.fontface |
Fontface for the x-axis scales |
yaxis.fontface |
Fontface for the y-axis scales |
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.tck |
Specifies the length of the tick marks for x-axis, defaults to 1 |
yaxis.tck |
Specifies the length of the tick marks for y-axis, defaults to 1 |
xlimits |
Two-element vector giving the x-axis limits |
ylimits |
Two-element vector giving the y-axis limits |
xat |
Vector listing where the x-axis labels should be drawn |
yat |
Vector listing where the y-axis labels should be drawn |
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 FALSE which draws panels from bottom left corner, moving right then up. Set to TRUE to draw from top left corner, moving right then down |
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 |
x.relation |
Allows x-axis scales to vary if set to “free”, defaults to “same” |
y.relation |
Allows y-axis scales to vary if set to “free”, defaults to “same” |
top.padding |
A number specifying the distance to the top margin, defaults to 0.5 |
bottom.padding |
A number specifying the distance to the bottom margin, defaults to 2 |
right.padding |
A number specifying the distance to the right margin, defaults to 1 |
left.padding |
A number specifying the distance to the left margin, defaults to 2 |
ylab.axis.padding |
A number specifying the distance of ylabel to the y-axis, defaults to 0 |
,
add.border |
Add xy border to polygon, default is FALSE |
add.xy.border |
DEPRECATED: Use 'add.border' argument instead |
add.median |
Add median line, default is FALSE |
median.lty |
Median line type |
median.lwd |
Median line width, defaults to 1.5 |
use.loess.border |
Use loess curve for border instead of max/min values, default is FALSE |
use.loess.median |
Use loess curve for median values, default is FALSE |
median |
Median values for median line |
median.col |
Median line colour, default is black |
extra.points |
If not set to NULL (default), add a set of extra points to the plot. A list of two numeric vectors named “x” and “y” giving the co-ordinates of the points to be added |
extra.points.pch |
A vector specifying the types of extra points to add to the plot. Defaults to 21 |
extra.points.type |
A vector specifying the plot type. Defaults to “p” |
extra.points.col |
A vector specifying the border colours of the extra points to add to the plot. Defaults to “black” |
extra.points.fill |
A vector specifying the fill colours of the extra points to add to the plot. Defaults to “white” |
extra.points.cex |
A vector specifying the sizes of the extra points to add to the plot. Defaults to 1 |
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 |
xgrid.at |
A vector listing the co-ordinates at which vertical grid-lines should be drawn. Default suppresses drawing of vertical grid-lines |
ygrid.at |
A vector listing the co-ordinates at which horizontal grid-lines should be drawn. Default suppresses drawing of horizontal grid-lines |
grid.lty |
Specifies the line type to use for the grid-lines. Defaults to 1 (solid lines) |
grid.col |
Specifies the colour to use for the grid-lines. Defaults to “grey” |
grid.lwd |
Specifies the width of the grid-lines. Defaults to 0.3 |
add.xyline |
Allow y=x line to be drawn, default is FALSE |
xyline.col |
y=x line colour, defaults to black |
xyline.lwd |
Specifies y=x line width, defaults to 1 |
xyline.lty |
Specifies y=x line style, defaults to 1 (solid) |
abline.h |
Allow horizontal line to be drawn, default to NULL |
abline.v |
Allow vertical line to be drawn, default to NULL |
abline.col |
Horizontal line colour, defaults to black |
abline.lwd |
Specifies horizontal line width, defaults to 1 |
abline.lty |
Specifies horizontal line style, defaults to 1 (solid) |
add.text |
Allow additional text to be drawn, default is FALSE |
text.labels |
Labels for additional text |
text.x |
The x co-ordinates where additional text should be placed |
text.y |
The y co-ordinates where additional text should be placed |
text.col |
The colour of additional text |
text.cex |
The size of additional text |
text.fontface |
The fontface for additional text |
key |
Add a key to the plot. See xyplot. |
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 |
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
Author(s)
Denise Mak
See Also
xyplot, lattice or the Lattice book for an overview of the package.
Examples
set.seed(12345);
temp <- matrix(runif(1010), ncol = 10) + sort(runif(101));
simple.data <- data.frame(
x = 0:100,
max = apply(temp, 1, max),
min = apply(temp, 1, min)
);
create.polygonplot(
# filename = tempfile(pattern = 'Polygon_Simple', fileext = '.tiff'),
formula = NA ~ x,
data = simple.data,
max = simple.data$max,
min = simple.data$min,
main = 'Simple',
xlimits = c(0,100),
ylimits = c (0,2),
col = default.colours(1),
description = 'Polygon created by BoutrosLab.plotting.general',
resolution = 100
);
# Compare two genes across increasing numbers of samples
data1 <- microarray[1,1:58];
data2 <- microarray[2,1:58];
gene1 <- as.data.frame(matrix(nrow = 58, ncol = 58));
gene2 <- as.data.frame(matrix(nrow = 58, ncol = 58));
fill.matrix <- function(x, gene, data){
for(i in x){
gene[i, 1:i] <- rep(NA, i);
gene[i, i:58] <- rep(as.numeric(data[i]), 58-i+1);
}
return(gene);
};
gene1 <- fill.matrix(1:58, gene1, data1);
gene1 <- t(matrix(unlist(gene1), ncol = 58, byrow = TRUE));
gene2 <- fill.matrix(1:58, gene2, data2);
gene2 <- t(matrix(unlist(gene2), ncol = 58, byrow = TRUE));
# Set up the data
polygon.data.gene1 <- data.frame(
x = 1:58,
max = apply(gene1, 2, function(x) {max(x, na.rm = TRUE)}),
median = apply(gene1, 2, function(x) {median(x, na.rm = TRUE)}),
min = apply(gene1, 2, function(x) {min(x, na.rm = TRUE)}),
set = rownames(microarray[1,]),
extra = apply(microarray[1:58], 2, function(x) {median(x)})
);
polygon.data.two.genes <- rbind(
polygon.data.gene1,
data.frame(
x = 1:58,
max = apply(gene2, 2, function(x) {max(x, na.rm = TRUE)}),
median = apply(gene2, 2, function(x) {median(x, na.rm = TRUE)}),
min = apply(gene2, 2, function(x) {min(x, na.rm = TRUE)}),
set = rownames(microarray[2,]),
extra = apply(microarray[1:58], 2, function(x) {median(x)})
)
)
# Minimal Input
create.polygonplot(
# filename = tempfile(pattern = 'Polygon_Minimal_Input', fileext = '.tiff'),
formula = NA ~ x,
data = polygon.data.gene1,
max = polygon.data.gene1$max,
min = polygon.data.gene1$min,
main = 'Minimal input',
xlimits = c(0,58),
ylimits = c (2,5),
description = 'Polygon created by BoutrosLab.plotting.general',
resolution = 100
);
# Axes & Labels
create.polygonplot(
# filename = tempfile(pattern = 'Polygon_Axes_Labels', fileext = '.tiff'),
formula = NA ~ x,
data = polygon.data.gene1,
max = polygon.data.gene1$max,
min = polygon.data.gene1$min,
main = 'Axes & labels',
xlimits = c(0,58),
ylimits = c (0,10),
# Axes & Labels
xlab.label = 'Samples',
ylab.label = 'Value',
xaxis.cex = 1,
yaxis.cex = 1,
xlab.cex = 1.5,
ylab.cex = 1.5,
xaxis.fontface = 1,
yaxis.fontface = 1,
xat = seq(0, 58, 5),
yat = seq(0, 10, 2),
description = 'Polygon created by BoutrosLab.plotting.general',
resolution = 100
);
# Colour
create.polygonplot(
# filename = tempfile(pattern = 'Polygon_Colour', fileext = '.tiff'),
formula = NA ~ x,
data = polygon.data.gene1,
max = polygon.data.gene1$max,
min = polygon.data.gene1$min,
main = 'Colour',
xlimits = c(0,58),
ylimits = c (0,10),
xlab.label = 'Samples',
ylab.label = 'Value',
xaxis.cex = 1,
yaxis.cex = 1,
xlab.cex = 1.5,
ylab.cex = 1.5,
xaxis.fontface = 1,
yaxis.fontface = 1,
xat = seq(0, 58, 5),
yat = seq(0, 10, 2),
# Colour
col = default.colours(1),
description = 'Polygon created by BoutrosLab.plotting.general',
resolution = 100
);
# Add median line and points
create.polygonplot(
# filename = tempfile(pattern = 'Polygon_Median_Points', fileext = '.tiff'),
formula = NA ~ x,
data = polygon.data.gene1,
max = polygon.data.gene1$max,
min = polygon.data.gene1$min,
# Median
median = polygon.data.gene1$median,
add.median = TRUE,
main = 'Plotting character',
xlimits = c(0,58),
ylimits = c (0,10),
xlab.label = 'Samples',
ylab.label = 'Value',
xaxis.cex = 1,
yaxis.cex = 1,
xlab.cex = 1.5,
ylab.cex = 1.5,
xaxis.fontface = 1,
yaxis.fontface = 1,
xat = seq(0, 58, 5),
yat = seq(0, 10, 2),
col = default.colours(1),
# border points
add.border = TRUE,
description = 'Polygon created by BoutrosLab.plotting.general',
resolution = 100
);
# Additional Data
create.polygonplot(
# filename = tempfile(pattern = 'Polygon_Extra_Data', fileext = '.tiff'),
formula = NA ~ x,
# divide data
groups = set,
data = polygon.data.two.genes,
max = polygon.data.two.genes$max,
min = polygon.data.two.genes$min,
main = 'Two data sets',
median = polygon.data.two.genes$median,
add.median = TRUE,
xlimits = c(0,58),
ylimits = c (0,15),
xlab.label = 'Samples',
ylab.label = 'Value',
xaxis.cex = 1,
yaxis.cex = 1,
xlab.cex = 1.5,
ylab.cex = 1.5,
xaxis.fontface = 1,
yaxis.fontface = 1,
xat = seq(0, 58, 5),
yat = seq(0, 14, 2),
# Increasing number of colours
col = default.colours(2),
description = 'Polygon created by BoutrosLab.plotting.general',
resolution = 100
);
# Legend
create.polygonplot(
# filename = tempfile(pattern = 'Polygon_Legend', fileext = '.tiff'),
formula = NA ~ x,
groups = set,
data = polygon.data.two.genes,
max = polygon.data.two.genes$max,
min = polygon.data.two.genes$min,
main = 'Legend',
median = polygon.data.two.genes$median,
add.median = TRUE,
xlimits = c(0,58),
ylimits = c (0,15),
xlab.label = 'Samples',
ylab.label = 'Value',
xaxis.cex = 1,
yaxis.cex = 1,
xlab.cex = 1.5,
ylab.cex = 1.5,
xaxis.fontface = 1,
yaxis.fontface = 1,
xat = seq(0, 58, 5),
yat = seq(0, 14, 2),
col = default.colours(2),
# Adding legend
key = list(
text = list(
lab = rownames(microarray[1:2,]),
cex = 0.8,
col = 'black'
),
points = list(
pch = 15,
col = default.colours(2),
cex = 2
),
x = 0.04,
y = 0.93,
padding.text = 3,
columns = 1
),
description = 'Polygon created by BoutrosLab.plotting.general',
resolution = 200
);
# Panel Organiation
create.polygonplot(
# filename = tempfile(pattern = 'Polygon_Panel', fileext = '.tiff'),
# divide data
formula = NA ~ x | set,
data = polygon.data.two.genes,
max = polygon.data.two.genes$max,
min = polygon.data.two.genes$min,
main = 'Panel',
median = polygon.data.two.genes$median,
add.median = TRUE,
xlimits = c(0,58),
ylimits = c (0,15),
xlab.label = 'Samples',
ylab.label = 'Value',
xaxis.cex = 1,
yaxis.cex = 1,
xlab.cex = 1.5,
ylab.cex = 1.5,
xaxis.fontface = 1,
yaxis.fontface = 1,
xat = seq(0, 58, 5),
yat = seq(0, 14, 2),
col = default.colours(1),
description = 'Polygon created by BoutrosLab.plotting.general',
resolution = 200
);
# Extra Points
create.polygonplot(
# filename = tempfile(pattern = 'Polygon_Extra_Points', fileext = '.tiff'),
formula = NA ~ x,
groups = set,
data = polygon.data.two.genes,
max = polygon.data.two.genes$max,
min = polygon.data.two.genes$min,
main = 'Extra points',
median = polygon.data.two.genes$median,
add.median = TRUE,
xlimits = c(0,58),
ylimits = c (0,15),
xlab.label = 'Samples',
ylab.label = 'Value',
xaxis.cex = 1,
yaxis.cex = 1,
xlab.cex = 1.5,
ylab.cex = 1.5,
xaxis.fontface = 1,
yaxis.fontface = 1,
xat = seq(0, 58, 5),
yat = seq(0, 14, 2),
col = default.colours(2),
# Add to legend
key = list(
text = list(
lab = c(rownames(microarray[1:2,]), 'All genes'),
cex = 0.8,
col = 'black'
),
points = list(
pch = c(15, 15, 3),
col = c(default.colours(2), 'red'),
cex = c(2, 2, 0.7)
),
x = 0.04,
y = 0.93,
padding.text = 3,
columns = 1
),
# Extra points
extra.points = list(
x = polygon.data.two.genes$x,
y = polygon.data.two.genes$extra
),
extra.points.col = 'red',
extra.points.pch = 3,
extra.points.type = c('p', 'l'),
extra.points.cex = 0.7,
description = 'Polygon created by BoutrosLab.plotting.general',
resolution = 200
);
# Nature style
create.polygonplot(
# filename = tempfile(pattern = 'Polygon_Nature_style', fileext = '.tiff'),
formula = NA ~ x,
groups = set,
data = polygon.data.two.genes,
max = polygon.data.two.genes$max,
min = polygon.data.two.genes$min,
main = 'Nature style',
median = polygon.data.two.genes$median,
add.median = TRUE,
xlimits = c(0,58),
ylimits = c (0,15),
xaxis.cex = 1,
yaxis.cex = 1,
xlab.cex = 1.5,
ylab.cex = 1.5,
xaxis.fontface = 1,
yaxis.fontface = 1,
xat = seq(0, 58, 5),
yat = seq(0, 14, 2),
col = default.colours(2),
# Adding legend
key = list(
text = list(
lab = rownames(microarray[1:2,]),
cex = 0.8,
col = 'black'
),
points = list(
pch = 15,
col = default.colours(2),
cex = 2
),
x = 0.04,
y = 0.93,
padding.text = 3,
columns = 1
),
# 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 = 'Polygon created by BoutrosLab.plotting.general',
resolution = 1200
);