| create.scatterplot {BoutrosLab.plotting.general} | R Documentation |
Make a scatterplot
Description
Takes a data.frame and creates a scatterplot
Usage
create.scatterplot(
formula,
data,
filename = NULL,
groups = 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,
xlimits = NULL,
ylimits = NULL,
xat = TRUE,
yat = TRUE,
xaxis.lab = NA,
yaxis.lab = NA,
xaxis.log = FALSE,
yaxis.log = FALSE,
xaxis.cex = 1.5,
yaxis.cex = 1.5,
xaxis.rot = 0,
yaxis.rot = 0,
xaxis.fontface = 'bold',
yaxis.fontface = 'bold',
xaxis.col = 'black',
yaxis.col = 'black',
xaxis.tck = c(1,1),
yaxis.tck = c(1,1),
add.grid = FALSE,
xgrid.at = xat,
ygrid.at = yat,
grid.colour = NULL,
horizontal = FALSE,
type = 'p',
cex = 0.75,
pch = 19,
col = 'black',
col.border = 'black',
lwd = 1,
lty = 1,
alpha = 1,
axes.lwd = 1,
strip.col = 'white',
strip.cex = 1,
strip.fontface = 'bold',
y.error.up = NULL,
y.error.down = y.error.up,
x.error.right = NULL,
x.error.left = x.error.right,
y.error.bar.col = 'black',
x.error.bar.col = y.error.bar.col,
error.whisker.angle = 90,
error.bar.lwd = 1,
error.bar.length = 0.1,
key = list(text = list(lab = c(''))),
legend = NULL,
top.padding = 0.1,
bottom.padding = 0.7,
right.padding = 0.1,
left.padding = 0.5,
key.top = 0.1,
key.left.padding = 0,
ylab.axis.padding = 1,
axis.key.padding = 1,
layout = NULL,
as.table = FALSE,
x.spacing = 0,
y.spacing = 0,
x.relation = 'same',
y.relation = 'same',
add.axes = FALSE,
axes.lty = 'dashed',
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.curves = FALSE,
curves.exprs = NULL,
curves.from = min(data, na.rm = TRUE),
curves.to = max(data, na.rm = TRUE),
curves.col = 'black',
curves.lwd = 2,
curves.lty = 1,
add.rectangle = FALSE,
xleft.rectangle = NULL,
ybottom.rectangle = NULL,
xright.rectangle = NULL,
ytop.rectangle = NULL,
col.rectangle = 'transparent',
alpha.rectangle = 1,
add.points = FALSE,
points.x = NULL,
points.y = NULL,
points.pch = 19,
points.col = 'black',
points.col.border = 'black',
points.cex = 1,
add.line.segments = FALSE,
line.start = NULL,
line.end = NULL,
line.col = 'black',
line.lwd = 1,
add.text = FALSE,
text.labels = NULL,
text.x = NULL,
text.y = NULL,
text.col = 'black',
text.cex = 1,
text.fontface = 'bold',
text.guess.labels = FALSE,
text.guess.skip.labels = TRUE,
text.guess.ignore.radius = FALSE,
text.guess.ignore.rectangle = FALSE,
text.guess.radius.factor = 1,
text.guess.buffer.factor = 1,
text.guess.label.position = NULL,
height = 6,
width = 6,
size.units = 'in',
resolution = 1600,
enable.warnings = FALSE,
description = 'Created with BoutrosLab.plotting.general',
style = 'BoutrosLab',
preload.default = 'custom',
group.specific.colouring = TRUE,
use.legacy.settings = FALSE,
inside.legend.auto = FALSE,
regions.labels = c(),
regions.start = c(),
regions.stop = c(),
regions.color = c("red"),
regions.cex = 1,
regions.alpha = 1,
lollipop.bar.y = NULL,
lollipop.bar.color = "gray",
...
);
Arguments
formula |
The formula used to extract the x & y components from the data-frame. Transforming data within formula is not compatible with automatic scaling with 'xat' or 'yat'. |
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 |
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 |
xlimits |
Two-element vector giving the x-axis limits, defaults to automatic |
ylimits |
Two-element vector giving the y-axis limits, defaults to automatic |
xat |
Accepts a vector listing where x-axis ticks should be drawn or if automatic scaling is desired, one of three strings: “auto”, “auto.linear” or “auto.log”. Automatic scaling fixes x-axis tick locations, labels, and data values dependent given data. “auto” will determine whether linear or logarithmic scaling fits the given data best, “auto.linear” or “auto.log” will force data to be scaled linearly or logarithmically respectively. Defaults to lattice automatic (TRUE). For more details see 'auto.axis()'. |
yat |
Accepts a vector listing where y-axis ticks should be drawn or if automatic scaling is desired, one of three strings: “auto”, “auto.linear” or “auto.log”. Automatic scaling fixes y-axis tick locations, labels, and data values dependent given data. “auto” will determine whether linear or logarithmic scaling fits the given data best, “auto.linear” or “auto.log” will force data to be scaled linearly or logarithmically respectively. Defaults to lattice automatic (TRUE). For more details see 'auto.axis()'. |
xaxis.lab |
Vector listing x-axis tick labels, defaults to automatic (TRUE). Using automatic scaling with xat will overwrite user input. Set to NULL to remove x-axis labels. |
yaxis.lab |
Vector listing y-axis tick labels, defaults to automatic (TRUE). Using automatic scaling with yat will overwrite user input. Set to NULL to remove y-axis labels. |
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.cex |
Size of x-axis scales, defaults to 2 |
yaxis.cex |
Size of y-axis scales, defaults to 2 |
xaxis.rot |
Counterclockwise rotation of text in x-axis scales in degrees, defaults to 0 |
yaxis.rot |
Counterclockwise rotation of text in y-axis scales in degrees, defaults to 0 |
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 mark, defaults to 1 for both top and bottom axes |
yaxis.tck |
Specifies the length of the tick mark, defaults to 1 for both top and bottom axes |
add.grid |
Logical stating wheter or not the grid should be drawn on the plot |
xgrid.at |
Vector listing where the x-axis grid lines should be drawn, defaults to xat |
ygrid.at |
Vector listing where the y-axis grid lines should be drawn, defaults to yat |
grid.colour |
ability to set individual grid line colours |
horizontal |
xyplot-specific function that allows you to change if type='h' draws lines to the vertical or horizontal axis |
type |
Plot type |
cex |
Character expansion for plotting symbol |
pch |
Plotting character |
col |
Point/line colour |
col.border |
Colour of border when points pch >= 21. Defaults to “black” |
lwd |
Specifies line width, defaults to 1 |
lty |
Specifies line style, defaults to 1 (solid) |
alpha |
Specifies line transparency, defaults to 1 (opaque) |
axes.lwd |
Thickness of width of axes lines |
strip.col |
Strip background colour, defaults to “white” |
strip.cex |
Strip title character expansion |
strip.fontface |
Strip title fontface, defaults to bold |
y.error.up |
upward error vector. Defaults to NULL. When y.error.up is NULL, vertical error bar is not drawn |
y.error.down |
Downward error vector. Defaults to y.error.down to show symmetric error bars |
x.error.right |
Rightward error vector. Defaults to NULL. When x.error.right is NULL, horizontal error bar is not drawn |
x.error.left |
Leftward error vector. Defaults to x.error.right to show symmetric error bars |
y.error.bar.col |
Colour of vertical error bar. Defaults to “black” |
x.error.bar.col |
Colour of horizontal error bar. Defaults to “black” |
error.whisker.angle |
Angle of the whisker drawn on error bar. Defaults to 90 degree |
error.bar.lwd |
Error bar line width. Defaults to 1 |
error.bar.length |
Length of the error bar whiskers. Defaults to 0.1 |
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. |
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 0.1 |
left.padding |
A number specifying the distance to the left margin, defaults to 0.5 |
key.top |
A number specifying the distance at top of key, defaults to 0.1 |
key.left.padding |
Amount of padding to go onto any legend on the left |
ylab.axis.padding |
A number specifying the distance of ylabel to the y-axis, defaults to 1 |
axis.key.padding |
A number specifying the distance from the y-axis to the key, 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 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” |
add.axes |
Allow axis lines to be turned on or off, default is FALSE |
axes.lty |
Specifies axis line style, defaults to “dashed” |
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.curves |
Allow curves to drawn, default is FALSE |
curves.exprs |
A list of functions, expressions, or calls using “x” as a variable that specify the curves to be drawn |
curves.from |
Specifies the x co-ordinates at which the start of each curve should be drawn, defaults to drawing the curves to the left edge of the plotting region |
curves.to |
Specifies the x co-ordinates at which the end of each curve should be drawn, defaults to drawing the curves to the right edge of the plotting region |
curves.col |
Specifies colours of curves, default is black for each curve |
curves.lwd |
Specifies width of curves, default is 1 for each curve |
curves.lty |
Specifies type of curves, default is 1 (solid) for each curve |
add.rectangle |
Allow a rectangle to be drawn, default is FALSE |
xleft.rectangle |
Specifies the left x ooordinate 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 rectangle's area |
alpha.rectangle |
Specifies the colour bias of the rectangle to be drawn |
add.points |
Allow additional points to be drawn, default is FALSE |
points.x |
The x co-ordinates where additional points should be drawn |
points.y |
The y co-ordinates where additional points should be drawn |
points.pch |
The plotting character for additional points |
points.col |
The colour of additional points |
points.col.border |
Colour of the border of additional points if points.pch >= 21. Defaults to black |
points.cex |
The size of additional points |
add.line.segments |
Allow additional line segments to be drawn, default is FALSE |
line.start |
The y co-ordinates where additional line segments should start |
line.end |
The y co-ordinates where additional line segments should end |
line.col |
The colour of additional line segments, default is black |
line.lwd |
The line width of additional line segments, default is 1 |
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 |
text.guess.labels |
Allows automatic labeling by considering values in text.x and text.y as a data point to be labelled, default is FALSE |
text.guess.skip.labels |
Provides an option to disregard automatic labelling algorithm if no space is available around a data point, thus forcing labelling if a collision is likely, default is TRUE |
text.guess.ignore.radius |
Allows the automatic labeling algorithm to ignore the radius space of a data point, useful to label a cluster of data points with a single text box, default is FALSE |
text.guess.ignore.rectangle |
Allows the atuomatic labeling algorithm to ignore the rectangle space of multiple potential label positions, default is FALSE |
text.guess.radius.factor |
A numeric value to factor the radius value to alter distance from the label and the data point |
text.guess.buffer.factor |
A numeric value to factor the buffer value to alter the space which is used to consider if data.points are potentially going to collide |
text.guess.label.position |
A numeric value between 0 and 360 to specify the percise angle of a text box center and the positive x-axis. Angles move counter-clockwise beginning at the positive x axis |
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 |
group.specific.colouring |
Variable to specify if group specific multi colouring for error bars is enforced |
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 |
regions.labels |
Labels for each of the regions on the lollipop plots bars |
regions.start |
start x value of each of the regions |
regions.stop |
stop value for each of the regions |
regions.color |
color of each of the regions |
regions.cex |
size of the text of each of the regions |
regions.alpha |
alpha of each of the regions |
lollipop.bar.y |
y location of top of the lollipop plot bar – defaults to right above the bottom y axis |
lollipop.bar.color |
color of the lollipop plot bar |
... |
Additional arguments to be passed to xyplot |
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)
Paul C. Boutros
See Also
xyplot, lattice or the Lattice book for an overview of the package.
Examples
set.seed(12345);
simple.data <- data.frame(
x = rnorm(800),
y = rnorm(800)
);
create.scatterplot(
# # filename = tempfile(pattern = 'Scatterplot_Simple', fileext = '.tiff'),
formula = y ~ x,
data = simple.data,
resolution = 50
);
scatter.data <- data.frame(
sample.one = microarray[1:800,1],
sample.two = microarray[1:800,2],
chr = microarray$Chr[1:800]
);
# Minimal Input
create.scatterplot(
# filename = tempfile(pattern = 'Scatterplot_Minimal_Input', fileext = '.tiff'),
formula = sample.two ~ sample.one,
data = scatter.data,
main = 'Minimal Input',
description = 'Scatter plot created by BoutrosLab.plotting.general',
resolution = 50
);
# Axes & Labels
create.scatterplot(
# filename = tempfile(pattern = 'Scatterplot_Axes_Labels', fileext = '.tiff'),
formula = sample.two ~ sample.one,
data = scatter.data,
main = 'Axes & Labels',
# Axes and labels
xlab.label = colnames(microarray[1]),
ylab.label = colnames(microarray[2]),
xat = seq(0, 16, 2),
yat = seq(0, 16, 2),
xlimits = c(0, 15),
ylimits = c(0, 15),
xaxis.cex = 1,
yaxis.cex = 1,
xaxis.fontface = 1,
yaxis.fontface = 1,
xlab.cex = 1.5,
ylab.cex = 1.5,
description = 'Scatter plot created by BoutrosLab.plotting.general',
resolution = 50
);
# Log-Scaled Axis
log.data <- data.frame(
x = rnorm(800),
y = 10 ** rnorm(800, mean = 5, sd = 2)
);
create.scatterplot(
formula = y ~ x,
data = log.data,
# Log base 10 scale y-axis
yat = 'auto.log',
main = 'Log Scaled',
description = 'Scatter created by BoutrosLab.plotting.general',
resolution = 50
);
# Colour & Plotting Character
create.scatterplot(
# filename = tempfile(pattern = 'Scatterplot_Colour_Pch', fileext = '.tiff'),
formula = sample.two ~ sample.one,
data = scatter.data,
main = 'Colour & Pch',
xlab.label = colnames(microarray[1]),
ylab.label = colnames(microarray[2]),
xat = seq(0, 16, 2),
yat = seq(0, 16, 2),
xlimits = c(0, 15),
ylimits = c(0, 15),
xaxis.cex = 1,
yaxis.cex = 1,
xaxis.fontface = 1,
yaxis.fontface = 1,
xlab.cex = 1.5,
ylab.cex = 1.5,
# setting the colour
col = default.colours(2)[2],
# setting the plotting character type & size
pch = 21,
cex = 1.5,
description = 'Scatter plot created by BoutrosLab.plotting.general',
resolution = 100
);
# Colour depth
# create colour scheme to illustrate adding a colourkey
chr.palette <- colour.gradient(default.colours(2)[2], 800);
create.scatterplot(
# filename = tempfile(pattern = 'Scatterplot_Colour_Depth', fileext = '.tiff'),
formula = sample.two ~ sample.one,
data = scatter.data,
main = 'Colour Depth',
xlab.label = colnames(microarray[1]),
ylab.label = colnames(microarray[2]),
xat = seq(0, 16, 2),
yat = seq(0, 16, 2),
xlimits = c(0, 15),
ylimits = c(0, 15),
xaxis.cex = 1,
yaxis.cex = 1,
xaxis.fontface = 1,
yaxis.fontface = 1,
xlab.cex = 1.5,
ylab.cex = 1.5,
# setting the colour
col = chr.palette,
# setting the plotting character type & size
pch = 19,
cex = 1,
# adding key for colours
key.top = 1.5,
legend = list(
bottom = list(
fun = draw.colorkey,
args = list(
key = list(
col = chr.palette,
at = 1:800,
tick.number = 3,
space = 'bottom',
size = 1,
width = 1.25,
height = 1,
labels = list(
labels = 1:3,
cex = 1,
at = c(1, which(scatter.data$chr == 2)[1], which(scatter.data$chr == 3)[1])
)
)
)
)
),
description = 'Scatter plot created by BoutrosLab.plotting.general',
resolution = 100
);
# Groups & Legend
create.scatterplot(
# filename = tempfile(pattern = 'Scatterplot_Groups_Legend', fileext = '.tiff'),
formula = sample.two ~ sample.one,
data = scatter.data,
main = 'Groups & Legend',
# using arbitrary groups for the sake of illustration
groups = scatter.data$chr,
xlab.label = colnames(microarray[1]),
ylab.label = colnames(microarray[2]),
xat = seq(0, 16, 2),
yat = seq(0, 16, 2),
xlimits = c(0, 15),
ylimits = c(0, 15),
xaxis.cex = 1,
yaxis.cex = 1,
xaxis.fontface = 1,
yaxis.fontface = 1,
xlab.cex = 1.5,
ylab.cex = 1.5,
col = default.colours(3),
# Adding legend for groups
key = list(
text = list(
lab = c('1','2','3'),
cex = 1,
col = 'black'
),
points = list(
pch = 19,
col = default.colours(3),
cex = 1
),
x = 0.04,
y = 0.95,
padding.text = 2
),
description = 'Scatter plot created by BoutrosLab.plotting.general',
resolution = 100
);
# Correlation Key
create.scatterplot(
# filename = tempfile(pattern = 'Scatterplot_Correlation_Key', fileext = '.tiff'),
formula = sample.two ~ sample.one,
data = scatter.data,
main = 'Correlation Key',
xlab.label = colnames(microarray[1]),
ylab.label = colnames(microarray[2]),
xat = seq(0, 16, 2),
yat = seq(0, 16, 2),
xlimits = c(0, 15),
ylimits = c(0, 15),
xaxis.cex = 1,
yaxis.cex = 1,
xaxis.fontface = 1,
yaxis.fontface = 1,
xlab.cex = 1.5,
ylab.cex = 1.5,
col = 'black',
pch = 21,
# Adding correlation key
legend = list(
inside = list(
fun = draw.key,
args = list(
key = get.corr.key(
x = scatter.data$sample.one,
y = scatter.data$sample.two,
label.items = c('spearman','spearman.p','kendall','beta1'),
alpha.background = 0,
key.cex = 1
)
),
x = 0.04,
y = 0.95,
corner = c(0,1)
)
),
description = 'Scatter plot created by BoutrosLab.plotting.general',
resolution = 100
);
# Panel Organization
create.scatterplot(
# filename = tempfile(pattern = 'Scatterplot_Panel_numeric_conditional', fileext = '.tiff'),
formula = sample.two ~ sample.one | chr,
data = scatter.data,
main = 'Panel',
xlab.label = colnames(microarray[1]),
ylab.label = colnames(microarray[2]),
xat = seq(0, 16, 2),
yat = seq(0, 16, 2),
xlimits = c(0, 15),
ylimits = c(0, 15),
xaxis.cex = 1,
yaxis.cex = 1,
xaxis.fontface = 1,
yaxis.fontface = 1,
xlab.cex = 1.5,
ylab.cex = 1.5,
pch = 21,
col = 'black',
fill = 'transparent',
# set up panel layout
layout = c(1,3),
yrelation = 'free',
description = 'Scatter plot created by BoutrosLab.plotting.general',
resolution = 100
);
scatter.data$chromosome <- as.character(scatter.data$chr);
create.scatterplot(
# filename = tempfile(pattern = 'Scatterplot_Panel_character_conditional', fileext = '.tiff'),
formula = sample.two ~ sample.one | chromosome,
data = scatter.data,
main = 'Panel',
xlab.label = colnames(microarray[1]),
ylab.label = colnames(microarray[2]),
xat = seq(0, 16, 2),
yat = seq(0, 16, 2),
xlimits = c(0, 15),
ylimits = c(0, 15),
xaxis.cex = 1,
yaxis.cex = 1,
xaxis.fontface = 1,
yaxis.fontface = 1,
xlab.cex = 1.5,
ylab.cex = 1.5,
pch = 21,
col = 'black',
fill = 'transparent',
# set up panel layout
layout = c(1,3),
yrelation = 'free',
description = 'Scatter plot created by BoutrosLab.plotting.general',
resolution = 100
);
# Covariates
cov.colours <- as.character(microarray$Chr[1:800]);
cov.colours[cov.colours == '1'] <- default.colours(3, palette.type = 'chromosomes')[1];
cov.colours[cov.colours == '2'] <- default.colours(3, palette.type = 'chromosomes')[2];
cov.colours[cov.colours == '3'] <- default.colours(3, palette.type = 'chromosomes')[3];
cov <- list(
rect = list(
col = 'transparent',
fill = cov.colours
)
);
cov.grob <- covariates.grob(
covariates = cov,
ord = c(1:length(cov.colours)),
side = 'top',
size = 1
);
cov.legend <- list(
legend = list(
colours = default.colours(3, palette.type = 'chromosomes'),
labels = c('1', '2', '3'),
title = 'Chromosome',
border = 'transparent'
)
);
cov.legend.grob <- legend.grob(
legends = cov.legend
);
create.scatterplot(
# filename = tempfile(pattern = 'Scatterplot_Covariates', fileext = '.tiff'),
formula = sample.two ~ sample.one,
data = scatter.data,
main = 'Covariates',
xlab.label = colnames(microarray[1]),
ylab.label = colnames(microarray[2]),
xat = seq(0, 16, 2),
yat = seq(0, 16, 2),
xlimits = c(0, 15),
ylimits = c(0, 15),
xaxis.cex = 1,
yaxis.cex = 1,
xaxis.fontface = 1,
yaxis.fontface = 1,
xlab.cex = 1.5,
ylab.cex = 1.5,
pch = 21,
col = 'black',
fill = 'transparent',
# Adding covariate & legend
legend = list(
bottom = list(fun = cov.grob),
right = list(fun = cov.legend.grob)
),
# Ensuring sufficient spacing for covariate
key.top = 3,
description = 'Scatter plot created by BoutrosLab.plotting.general',
resolution = 200
);
# Error bars
error.data <- data.frame(
chr = (microarray$Start)[1:20],
values = apply(microarray[1:20,1:58], 1, mean),
error = apply(microarray[1:20,1:58], 1, sd)
);
create.scatterplot(
# filename = tempfile(pattern = 'Scatterplot_Error_Bars', fileext = '.tiff'),
formula = values ~ chr,
data = error.data,
main = 'Error Bars',
xlab.label = 'Base pair location on chromosome one',
ylab.label = 'Gene expression change',
# xat = seq(0, 16, 2),
yat = seq(0, 14, 2),
# xlimits = c(0, 15),
ylimits = c(0, 13),
# Format xaxes
xaxis.lab = c(
scientific.notation(0, 1),
scientific.notation(1000000, 1),
scientific.notation(2000000, 1),
scientific.notation(3000000, 1),
scientific.notation(4000000, 1),
scientific.notation(5000000, 1),
scientific.notation(6000000, 1),
scientific.notation(7000000, 1)
),
xaxis.rot = 90,
xaxis.cex = 1,
yaxis.cex = 1,
xaxis.fontface = 1,
yaxis.fontface = 1,
xlab.cex = 1.5,
ylab.cex = 1.5,
pch = 19,
col = 'black',
fill = 'transparent',
# Specifying error bars
error.bar.lwd = 1,
error.whisker.angle = 120,
y.error.up = error.data$error,
y.error.bar.col = 'black',
description = 'Scatter plot created by BoutrosLab.plotting.general',
resolution = 200
);
create.scatterplot(
# filename = tempfile(pattern = 'Scatterplot_Error_Bars_MultiColor', fileext = '.tiff'),
formula = values ~ chr,
data = error.data,
main = 'Error Bars',
xlab.label = 'Base pair location on chromosome one',
ylab.label = 'Gene expression change',
# xat = seq(0, 16, 2),
yat = seq(0, 14, 2),
# xlimits = c(0, 15),
ylimits = c(0, 13),
# Format xaxes
xaxis.lab = c(
scientific.notation(0, 1),
scientific.notation(1000000, 1),
scientific.notation(2000000, 1),
scientific.notation(3000000, 1),
scientific.notation(4000000, 1),
scientific.notation(5000000, 1),
scientific.notation(6000000, 1),
scientific.notation(7000000, 1)
),
xaxis.rot = 90,
xaxis.cex = 1,
yaxis.cex = 1,
xaxis.fontface = 1,
yaxis.fontface = 1,
xlab.cex = 1.5,
ylab.cex = 1.5,
pch = 19,
col = 'black',
fill = 'transparent',
# Specifying error bars
error.bar.lwd = 1,
error.whisker.angle = 120,
y.error.up = error.data$error,
y.error.bar.col = c('black','red','blue'),
description = 'Scatter plot created by BoutrosLab.plotting.general',
group.specific.colouring = FALSE,
resolution = 200
);
# Gridlines
create.scatterplot(
# filename = tempfile(pattern = 'Scatterplot_Gridlines', fileext = '.tiff'),
formula = sample.two ~ sample.one,
data = scatter.data,
main = 'Gridlines',
xlab.label = colnames(microarray[1]),
ylab.label = colnames(microarray[2]),
xat = seq(0, 16, 2),
yat = seq(0, 16, 2),
xlimits = c(0, 15),
ylimits = c(0, 15),
xaxis.cex = 1,
yaxis.cex = 1,
xaxis.fontface = 1,
yaxis.fontface = 1,
xlab.cex = 1.5,
ylab.cex = 1.5,
pch = 21,
col = 'black',
fill = 'transparent',
# Adding gridlines
type = c('p','g'),
description = 'Scatter plot created by BoutrosLab.plotting.general',
resolution = 200
);
# lines & background rectangle
create.scatterplot(
# filename = tempfile(pattern = 'Scatterplot_Lines_BG', fileext = '.tiff'),
formula = sample.two ~ sample.one,
data = scatter.data,
main = 'Lines & BG rectangle',
xlab.label = colnames(microarray[1]),
ylab.label = colnames(microarray[2]),
xat = seq(0, 16, 2),
yat = seq(0, 16, 2),
xlimits = c(0, 15),
ylimits = c(0, 15),
xaxis.cex = 1,
yaxis.cex = 1,
xaxis.fontface = 1,
yaxis.fontface = 1,
xlab.cex = 1.5,
ylab.cex = 1.5,
pch = 21,
col = 'black',
fill = 'transparent',
type = c('p','g'),
# add xy line
add.xyline = TRUE,
xyline.lty = 3,
xyline.col = 'red',
xyline.lwd = 3,
# add background rectangle
add.rectangle = TRUE,
xleft.rectangle = which(scatter.data$chr == 2)[1]/800*15,
xright.rectangle = which(scatter.data$chr == 3)[1]/800*15,
ybottom.rectangle = 0,
ytop.rectangle = 15,
col.rectangle = 'grey',
alpha.rectangle = 0.5,
description = 'Scatter plot created by BoutrosLab.plotting.general',
resolution = 200
);
# attach lines to points
create.scatterplot(
# filename = tempfile(pattern = 'Scatterplot_Lines', fileext = '.tiff'),
formula = sample.two ~ sample.one | chr,
data = scatter.data,
main = 'Lines',
xlab.label = colnames(microarray[1]),
ylab.label = colnames(microarray[2]),
xat = seq(0, 16, 2),
yat = seq(0, 16, 2),
xlimits = c(0, 15),
ylimits = c(0, 15),
xaxis.cex = 1,
yaxis.cex = 1,
xaxis.fontface = 1,
yaxis.fontface = 1,
xlab.cex = 1.5,
ylab.cex = 1.5,
pch = 21,
col = 'black',
fill = 'transparent',
# attach lines
type = c('h','p'),
layout = c(1,3),
description = 'Scatter plot created by BoutrosLab.plotting.general',
resolution = 200
);
# ROC curve
set.seed(123456);
class.values <- runif(50, 0, 1);
observed.values <- sample(c(0,1), size = 50, replace = TRUE);
cutoffs <- seq(1,0,-0.01);
tprs <- c();
fprs <- c();
for (c in cutoffs) {
roc.classification <- rep(0, length(class.values));
roc.classification[class.values >= c] <- 1;
roc.results <- table(
factor(roc.classification, levels = c(0,1)),
factor(observed.values, levels = c(0,1)),
dnn = c('pred', 'obs')
);
tprs <- c(tprs, roc.results[2,2] / (roc.results[2,2] + roc.results[1,2]));
fprs <- c(fprs, roc.results[2,1] / (roc.results[2,1] + roc.results[1,1]));
}
roc.data <- data.frame(cutoff = cutoffs, TPR = tprs, FPR = fprs);
points.x <- roc.data[match(c(0.25, 0.5, 0.75), roc.data$cutoff), 'FPR'];
points.y <- roc.data[match(c(0.25, 0.5, 0.75), roc.data$cutoff), 'TPR'];
create.scatterplot(
# filename = tempfile(pattern = 'Scatterplot_ROC', fileext = '.tiff'),
formula = TPR ~ FPR,
data = roc.data,
main = 'ROC',
xlab.label = 'False positive rate',
ylab.label = 'True positive rate',
xaxis.cex = 1,
yaxis.cex = 1,
xaxis.fontface = 1,
yaxis.fontface = 1,
xlab.cex = 1.5,
ylab.cex = 1.5,
type = 's',
lwd = 3,
add.xyline = TRUE,
xyline.col = 'grey',
add.points = TRUE,
points.x = points.x,
points.y = points.y,
points.col = c('blue', 'darkgreen', 'red'),
add.text = TRUE,
text.labels = paste('cutoff = ', c(0.25, 0.5, 0.75), sep = ''),
#text.x = points.x - 0.14,
#text.y = points.y + 0.03,
text.x = points.x,
text.y = points.y,
text.guess.labels = TRUE,
text.guess.label.position = 155,
text.guess.radius.factor = 2.5,
description = 'Scatter plot created by BoutrosLab.plotting.general',
resolution = 200
);
# Volcano Plots
fold.change <- apply(microarray[,1:29], 1, mean) - apply(microarray[,30:58], 1, mean);
fake.microarray <- microarray[,1:58] - log(mean(apply(microarray[,1:58],1, mean)));
fake.microarray[,30:58] <- fake.microarray[,30:58] + mean(fold.change);
fake.microarray[fake.microarray < 0] <- 0;
p.values <- apply(fake.microarray[,1:58], 1, function(x) {t.test(x=x[1:29],y=x[30:58])$p.value} );
fold.change <- apply(fake.microarray[, 1:29], 1, mean) - apply(fake.microarray[, 30:58], 1,mean);
p.values.adjusted <- p.adjust(p.values, 'fdr');
dot.colours <- vector(length=length(p.values));
dot.colours[p.values.adjusted < .05 & fold.change < 0] <- 'green';
dot.colours[p.values.adjusted < .05 & fold.change > 0] <- 'red';
dot.colours[p.values.adjusted > .05] <- 'black';
volcano.data <- data.frame(
p.values = -log10(p.values.adjusted),
fold.change = fold.change
);
create.scatterplot(
# filename = tempfile(pattern = 'Scatterplot_Volcano_Plot', fileext = '.tiff'),
formula = p.values ~ fold.change,
data = volcano.data,
col = dot.colours,
alpha = .5,
yat = c(0,2,4,6,8),
ylimits = c(-0.1,8.1),
yaxis.lab = expression(10^0,10^-2,10^-4,10^-6,10^-8),
yaxis.cex = 1.5,
xaxis.cex = 1.5,
xlab.label = 'foldChange',
ylab.label = 'pValues',
xlab.cex = 1.75,
ylab.cex = 1.75,
resolution = 200
);
# Automatic Labeling
interesting.fold.change <- (fold.change < -.9 | fold.change > .9);
interesting.p.value <- (-log10(p.values.adjusted) < 8 & -log10(p.values.adjusted) > 2);
interesting.points <- interesting.fold.change & interesting.p.value;
text.x <- fold.change[interesting.points];
text.y <- (-log10(p.values.adjusted))[interesting.points];
text.labels <- rownames(microarray)[interesting.points];
create.scatterplot(
# filename = tempfile(pattern = 'Scatterplot_Volcano_Plot_With_Labels', fileext = '.tiff'),
formula = p.values ~ fold.change,
data = volcano.data,
alpha = .5,
yat = c(0,2,4,6,8),
ylimits = c(-0.1,8.1),
xlimits = c(-1.5,1.5),
yaxis.lab = expression(10^0,10^-2,10^-4,10^-6,10^-8),
yaxis.cex = 1.5,
xaxis.cex = 1.5,
xlab.label = 'foldChange',
ylab.label = 'pValues',
xlab.cex = 1.75,
ylab.cex = 1.75,
add.text = TRUE,
text.x = text.x,
text.y = text.y,
text.labels = text.labels,
text.guess.labels = TRUE,
resolution = 200
);
# With line segments
line.data <- data.frame(
group = as.factor(c('A','B','C')),
x = sample(1:10,3),
y = sample(1:10,3),
z = sample(1:10,3)
);
create.scatterplot(
(x+y+z) ~ group,
line.data,
# filename = tempfile(pattern = 'Scatterplot_with_LineSegments', fileext = '.tiff'),
cex = 0,
add.line.segments = TRUE,
line.start = list(
rep(0,nrow(line.data)),
line.data$x,
c(line.data$x + line.data$y)
),
line.end = list(
line.data$x,
c(line.data$x + line.data$y),
c(line.data$x + line.data$y + line.data$z)
),
line.col = list('red','blue','green'),
line.lwd = list(3,3,3),
resolution = 200
);
lollipop.data <- data.frame(
y = seq(1,100,1),
x = rnorm(100)
);
create.lollipopplot(
# filename = tempfile(pattern = 'Lollipop_Simple', fileext = '.tiff'),
formula = x ~ y,
data = lollipop.data,
main = 'Lollipop plot',
xaxis.cex = 1,
xlimits = c(-1,102),
yaxis.cex = 1,
xaxis.fontface = 1,
yaxis.fontface = 1,
xlab.cex = 1.5,
ylab.cex = 1.5,
pch = 21,
col = 'black',
fill = 'transparent',
description = 'Scatter plot created by BoutrosLab.plotting.general',
regions.start = c(1,26,48),
regions.stop = c(15,35,72),
regions.labels = c("test 1", "test2", "test 3"),
regions.color = c("#66b3ff", "#5cd65c", "#ff3333"),
resolution = 200
);