R_ versions of Free,
Calloc, and Realloccreate.scatterplotcreate.scatterplotcreate.boxplotcreate.manhattanplotcreate.hexbinplotcreate.barplotprint.multipanelmultipanelplotscreate.histogramcreate.boxplot for consistent behavior with other plot
typescreate.histogrammultipanelplot
labels and maincreate.violinplot.Rdcreate.boxplotcreate.polygonplotcreate.polygonplot()create.boxplot to print different text label on
each panelcreate.boxplotcreate.heatmapcreate.multiplot and
create.multipanel that wasn’t passing CRAN’s check by
changing ‘is.na’ to ‘anyNA’create.multiplot that was only checking
the first element in a list by using ‘is.element’ instead of ‘==’create.hexbinplot: added option to modify the default
legend titlecreate.polygonplotcreate.scatterplot preventing
automatic axis determination when all y == 0 or all y == -Nmultipanelplot now saves temp plots to temp dirmultipanelplot code and ## Changedd the
examplesmultipanelplot legend/label placement algorithm
more optimalcreate.multiplot function
(create.multipanelplot)*pcawg.colours: new and renamed tumour type names added to palette, sv class ‘insertion’ assigned colour
create.heatmap - grid row/column limits reversedcreate.scatterplot() doesn’t work
properly.create.multiplotcreate.heatmapcreate.gif for creating animated plotscreate.barplot.R: fixed a ## Fixed interfering with
add.rectangle and ## Removed redundant add.background.shading (repeats
add.rectangle functionality)create.barplot.R: minor improvements to some
exampleslwd into axes.lwd and
border.lwd to be consistent with other functionsremove.all.border.lines as this can
now be accomplished with axes.lwdcreate.violinplot: fixed a ## Fixed in colour
functionality; now repeats colours when fewer colours are supplied than
there are groupscreate.hexbinplot: changed argument abline.type to
abline.lty to be consistent with other functionscreate.segplot: added warning for specific use case
(multiplot fails when a vertical segplot is the first plot)create.manhattanplot: changed argument axis.lwd to
axes.lwd to be consistent with other functionscreate.hexbinplot, create.histogram,
create.manhattanplot, create.polygonplot,
create.qqplot.comparison, create.qqplot.fit,
create.scatterplot, create.stripplot,
create.segplot, create.violinplot,
age.categorical.colour, append.footnote: applied code formatting (BL
standards)*create.multiplot: Added functionality to add top x-axis
tick labels. Has not been extensively tested.
*pcawg.colours: fixed ## Fixed that prevented project code colours from being returned.
*create.dotmap: addition of parameters for rectangle
border thickness, rectangle border colour.
create.scatterplot: adding conditional for when pch is
not referring to a point (this is in reference to KM plots)create.scatterplot: addition of parameter “col.border”.
This allows customizable border colours when pch >= 21.create.polygonplot: option to add rectangles.create.heatmap: rotation of the top x axis labels is
now independent from the bottom x axsis labels.create.multiplot: options to set the distance between
tick marks and tick labelscreate.polygonplot: option to add text.create.polygonplot: added parameters alpha and
median.lwd.create.densityplot &
create.violinplot: allow adjustment of bandwidth with
parameters bandwidth and bandwidth.adjust.create.stripplot: allow different border colour for
added points when pch >= 21create.scatterplot: allow different border colour for
added points when pch >= 21create.dotmap: Added parameters ‘columns’ and ‘rows’
for spot.colour.function to allow dots colours to be grouped by columns
or rows, respectively [BPG-16]. There are 12 distinct colours (the
default colours) and the colours start to repeat when there are more
than 12 columns/rows. It also checks that the columns/rows (depending on
which side is selected) are unique and throws and error if they are
not.create.multiplot: fixed ## Fixed where NULL values in
parameter list (for xlimits=/ylimits=) were being ignored/unprocessed
[BPG-2].create.barplot: Added parameters ‘add.text’, ‘text.x’,
‘text.y’, ‘text.labels’, ‘text.col’, ‘text.cex’, ‘text.fontface’ to
allow users to add text labels to plot area. Added parameter ‘box.ratio’
for adjusting thickness of each bar. Added parameter
‘remove.all.border.lines’ to allow barplots with no borders. Added
example for adding text to plot and adjusting box.ratio.create.barplot: fixed adding error bars for data-frames
[BPG-4]create.boxplot: Added example for adding text to
plot.create.hexbinplot: Added example of stratified
multiplot.create.dotmap: NA plotting character can be made
different colours with new variable, NA.spot.size.colour. Default is set
to black.create.multiplotcreate.scatterplot: added option to specify colour of
grid lines.create.heatmap: turns off grid lines when row or column
number exceeds a certain threshold.BoutrosLab.plotting.general 5.3.7
create.boxplot by max, min, mean
and median (defaults to median if not set)create.scatterplot: ## Changedd ROC example to use
auto-label placementcreate.heatmap: fixed ## Fixed which made labels
disappear when stratifying dendrogramcreate.hexbinplot: added add.xyline and add.curves
functionality (same as in create.scatterplot)create.barplot, create.boxplot,
create.hexbinplot, create.manhattanplot,
create.polygonplot, create.scatterplot,
create.segplot, create.stripplot,
create.violinplot: Set xlab.label and ylab.label to default
to formula componentscreate.multiplot: added example showing how to save
parameter options from individual plotscreate.heatmap: Added two parameters: text.position and
text.offset to customize placement of text in cellscreate.heatmap (more robust method)create.hexbinplot: added comment to explain maxcnt
removing datapoints from example plotcreate.barplot: allow vector of custom sorting order
for samplescreate.multiplot: has flag to remove all border lines
from plotscreate.barplot: ablines now appear in the background of
the plot instead of the foregroundcreate.scatterplot: for add.line.segments, changed
line-end style to ‘butt’create.stripplot: NEW ARGUMENTS to allow for addition
of lines showing group medianscreate.boxplot: added arguments to allow for addition
of stripplot in backgroundcreate.scatterplot: changed argument name - add.lines
> add.line.segmentscreate.scatterplot: ## Changedd to accept lists of line
segments to addcreate.manhattanplot: ## Changedd documentation to use
chromosome palette in force.colour.schemecreate.barplot: changed default fill colour to black
(instead of grey)create.scatterplot: NEW ARGUMENTS text.guess.* now
allows users to specify data points so that associated label positions
can be automatically determinedcreate.scatterplotcreate.heatmap: NEW ARGUMENT gridline.order now allows
user to specify in which order gridlines should be drawn (horizontal or
vertical first)create.scatterplot, add.lines now works with
lists of datacreate.scatterplot:
create.scatterplot:
create.stripplot:
create.dotmap clustered by dots and
dendrogram addedcreate.barplot:
create.histogram: Silenced warning caused by data
parametercreate.scatterplot.with.error: ## Removed function,
merged with create.scatterplotcreate.multiple.stripplots: ## Removed function,
functionality contained within create.stripplotcreate.multiple.boxplots: ## Removed function,
functionality contained within create.boxplotcreate.barplot.with.error: ## Removed function,
functionality contained within create.barplotcreate.violinplot: Renamed function from
create.violin.plotcreate.polygonplot: Renamed function from
create.polygoncreate.multiplot: ## Changedd example plots to use
standard datasetcreate.scatterplot: Added example using error barscreate.violin.plot: ## Changedd example plots to use
standard datasetcreate.stripplot: ## Changedd example plots to use
standard datasetcreate.stripplot: Exposing xat and xlimits parameter to
allow for customization of horizontal plotscreate.segplot: ## Changedd example plots to use
standard datasetcreate.scatterplot: ## Changedd example plots to use
standard datasetcreate.manhattanplot examplescreate.colourkey: Fixed formatting in documentation to
fit under 90 characters per linecreate.histogram: ## Changedd example code to check
dataset size instead of use hard-coded valuescreate.colourkey: Exposed parameter for colourkey
cexcreate.qqplot.fit: ## Changedd example plots to use
standard datasetcreate.qqplot.comparison: ## Changedd example plots to
use standard datasetcreate.polygon: ## Changedd example plots to use
standard datasetcreate.histogram: ## Changedd example plots to use
standard datasetcreate.hexbinplot: ## Changedd example plots to use
standard datasetcreate.dotmap: ## Changedd example plots to use
standard datasetcreate.densityplot: ## Changedd example plots to use
standard datasetcreate.boxplot: ## Changedd example plots to use
standard datasetcreate.heatmap: ## Changedd example plots to use
standard datasetcreate.heatmap: Fixed error where heatmap threw error
if symbols were added, but not ‘border’ symbolscreate.heatmap: Added clarification to documentation
that ‘colour.alpha’ can be set to ‘automatic’create.multiplot: Expose parameters for x-axis and
y-axis tick mark lengthscreate.violinplot: ## Removed error message for using
pch>=21 with lattice version 20-13create.violinplot: Modified handling of border and fill
colours for extra pointscreate.manhattanplot: ## Changedd example plots to use
standard datasetcreate.barplot: ## Changedd example plots to use
standard datasetcreate.dotmap: enabled default behaviour for NA values
to plot ‘X’ characters size 7create.dotmap: Improved handling of multiple pch with
multiple fill colourscreate.dotmap: Deleted warning for using pch>=21
with lattice version 20-13 (outdated)create.dotmap: Stopped printing of warning regarding
using pch>=21 with lattice version 20-13create.hexbinplot: Fixed formatting issuecreate.scatterplot: Fixed auto-sensing of labelscreate.barplot: Added functionality of adding text
above barscreate.heatmap: Added ability to have multi-sized
borderscreate.heatmap: Adjusted input of ‘main’ to accept
non-list valuescreate.densityplot: Added data-sensingcreate.scatterplot: Added data-sensingcreate.hexbinplot: Added example of multi-colour
schemecreate.densityplot: Expose top, bottom, left, and right
padding parameterscreate.hexbinplot: Expose top, bottom, left, and right
padding parameterscreate.qqplot.fit: Expose top, bottom, left, and right
padding parameterscreate.qqplot.comparison: Expose top, bottom, left, and
right padding parameterscreate.violin.plot: Expose top, bottom, left, and right
padding parameterscreate.heatmap: Added removal of top bar in stratified
dendrogramscreate.heatmap: Fixed coding issuescreate.heatmap: Added ability to automatically estimate
values for colour.alpha parametercreate.heatmap: Added example for automatic
colour.alpha value estimationcreate.heatmap: Fixed grid to also draw lines on first
row & columncreate.barplot: Fixed default units to inchescreate.heatmap: Fixed documentation to match changes in
codecreate.boxplot: Fixed naming issuecreate.multiplot: Fixed naming conventionscreate.heatmap: Added ability to stratify
dendrogramcreate.boxplot: Added ability to reorder boxplots based
on median valuescreate.barplot: Added ability to draw curvescreate.boxplot: Added ability to draw curvescreate.barplot.with.error: Adjusted whisker length to
not cover whole barcreate.heatmap: Added example of per-cell font
characteristicscreate.barplot: Added example of grouped labelscreate.boxplot: Added option of drawing line either in
front of or behind plotcreate.heatmap: Fixed issue with symbolscreate.heatmap: Added global covariate outlinecreate.barplot: Added grouping of labels for grouped
barplotcreate.heatmap: Added examplescreate.multiplot: Added examplescreate.multiplot: Added ability to retrieve plot labels
& limits from ‘original’ plotscreate.multiplot: ## Changedd examplescreate.heatmap: Added functionality of inserting
additional symbolscreate.heatmap: Added example to documentation of
symbol usagecreate.scatterplot: Changed ablines to be drawn in
front of plotcreate.barplot: Fixing reordering of barscreate.barplot: Set default reordering to FALSEcreate.dotmap: Added functionality to change dot
colourcreate.barplot: Added functionality to reorder bars to
be increasing or decreasingcreate.hexbinplot: Added more examplescreate.hexbinplot: Added background colourcreate.hexbinplot: Added ability to have tick marks on
top x axis onlycreate.hexbinplot: Enabled svg outputcreate.hexbinplot: Added examples to documentationcreate.barplot: ## Removed origin from panel call to
enable creation of stacked, horizontal, unidirectional plotscreate.hexbinplot: Added ability to change background
colourcreate.heatmap: Added ability to display tick marks on
top axis onlycreate.manhattanplot functioncreate.boxplot: Added ability to draw rectangle
panelscreate.boxplot: Added new example with grey shading
between different boxescreate.barplot: Added ability to change the width of
the boxcreate.barplot: Added new parameters - background.col
and draw.gridcreate.barplot: Added new example of grey background
with white grid linescreate.colourkey to NAMESPACEcreate.barplot: ## Changedd manual to reflect addition
of ‘axis.fontface’ argumentcreate.colourkey: ## Removed ‘enable.warnings’
argumentcreate.barplot: Added arguments ‘xaxis.fontface’ and
‘yaxis.fontface’create.colourkey’ to generate and
draw colourkeycreate.stripplot: New arguments ‘xaxis.fontface’,
‘yaxis.fontface’ to allow for modification of axis tck label font
facecreate.stripplot: New argument ‘ylab.axis.padding’
allows for modification of padding between yaxis label and tck
labelscreate.dendrogram: ## Changedd documentation for
jaccard usagecreate.heatmap: ## Changedd documentation for jaccard
usagecreate.heatmap: Moved logic for x.tck out of level
plotcreate.heatmap: Refactoring and cleanup of codecreate.polygon: Added ‘median.lty’ (for seq power
plot)create.hexbinplot: Changed default of ‘mincnt’ to 1
(from 0)create.scatterplot.with.error: New arguments to specify
plot layout and placement - ‘layout’, ‘as.table’, ‘x.spacing’,
‘y.spacing’create.polygon: Added parameters ‘axis.log’ and
‘yaxis.log’create.dotmap: Added examplecreate.multiplot: ## Changedd documentationcreate.scatterplot: Added parameter ‘axis.key.padding’
to adjust spacing between y-axis and keycreate.scatterplot: Added parameters ‘add.points’,
‘points.x’, ‘points.y’, ‘points.col’, ‘points.pch’, ‘points.cex’ - allow
users to add additional points to plot areacreate.scatterplot: Added parameters ‘add.text’,
‘text.x’, ‘text.y’, ‘text.labels’, ‘text.col’, ‘text.cex’,
‘text.fontface’ - allow users to add text labels to plot areacreate.dotmap: Added padding parametercreate.barplot: Adjustments to spacing and
commentingcreate.dotmap: Added ability to specify padding on all
sides of plotcreate.multiplot: New argument ‘axes.lwd’ to specify
border line thicknesscreate.multiplot: Fixed ‘xlab.to.xaxis.padding’
variable to change the correct parametercreate.heatmap: Added ability to specify two x-axes,
and gave meaning to ‘x-alternating = 3’ (prints tick marks on top and
bottom x axes)create.multiplot: Added ‘xlab.to.xaxis.padding’
parametercreate.dotmap: Replaced ‘grid.colour’ with ‘row.colour’
and ‘col.colour’create.barplot: ## Changedd to accept arguments that
handle background shadingcreate.heatmap: Added ‘xaxis.tck’ and ‘yaxis.tck’
parameters to override default values based on covariate sizecreate.multiplot: Added ‘layout.skip’ parameter to
allow for blank spots in layout, and also added a complex examplecreate.boxplot: Added ability to define ‘abline.v’create.heatmap: Added ‘covariates.reorder.grid.index’
and ‘covariates.top.reorder.grid.index’ parameters to match changes to
covariates.grobcreate.heatmap: Split ‘grid.colour’ and ‘grid.lwd’
parameters into ‘row.colour/col.colour’ and ‘row.lwd/col.lwd’create.heatmap: Added grandfather parameters for
‘grid.colour’ and ‘grid.lwd’create.heatmap: Added ‘covariates.row.lines’,
‘covariates.col.lines’, ‘covariates.top.row.lines’,
‘covariates.top.col.lines’ corresponding to new covariates.grob
arguments, and ## Changedd examplescreate.barplot: Attempting to make sizes match upcreate.dotmap: Can now have custom colours
specifiedcreate.barplot: Code clean-up to match coding
standardscreate.barplot: Fix to align error bars when barplot is
groupedcreate.segplot: Added ‘abline.h’ parametercreate.heatmap: Centralize parameter-checking code at
start of scriptcreate.polygon: Added line plotting options
‘add.xyline’, ‘abline.h’, ‘abline.v’create.barplot: Added examplescreate.multiplot: Added check for NAs in the legends
workaroundcreate.multiplot: Added workaround for lattice being
unable to accept multiple legends with the same name via ##
Changed.trelliscreate.multiplot: Allowed x/y-relations between plots
to be setcreate.multiplot: Added ‘xlab.padding’, and
‘key.bottom.padding’create.barplot: Updating with “raster” commandcreate.multiplot: Making examples prettier, moving
key.bottom.padding into argumentcreate.barplot: Merging with
create.barplot.with.errorcreate.barplot.with.error: Merging with
create.barplotcreate.scatterplot: Added explicit horizontal
argumentcreate.barplot: Added options to specify distance
between x-axis and labelcreate.scatterplot: Add options to pass arbitrary plots
onto lattice:xyplotcreate.barplot.with.error: Fixing documentationcreate.barplot: Allow user to edit ‘key.bottom’create.stripplot: Added parameters to allow for
different border/fill colours (for pch 21:25), ‘colour.alpha’ to allow
for plotting character transparencies, ‘as.table’, ‘x.spacing’,
‘y.spacing’ for customization of panelscreate.dotmap: Added argument ‘pch.border.col’ to set
colour of dot border if pch is 21:25create.scatterplot: Added ‘key.left.padding’ parameter
to place legends to left of graphcreate.scatterplot: Added ‘axes.lty’ to set line style
of axes linescreate.multiplot: Added three parameters - ‘xaxis.rot’,
‘key.left.padding’, ‘key.right.padding’create.heatmap: Added option of including x and y axis
label covariates (between label and heatmap), and examplescreate.multiplot: Changed key.left value to 1 so that
legends can be placed to left of multiplot areacreate.scatterplot: Added ability to draw rectangles in
backgroundcreate.polygon: Changed default values of ‘xgrid.at’
and ‘ygrid.at’create.polygon: Added ‘xaxis.fontface’ and
‘yaxis.fontface’create.polygon: Added ‘fontface = xaxis.fontface’ and
‘fontface = yaxis.fontface’ to scales\(x and
scales\)ycreate.polygon: Added example to demonstrate use with
legend.grobcreate.polygon: Adjusted values of par.settings\(layout.widths\)axis.key.padding and
par.settings\(layout.heights\)axis.key.padding to equal 1
- this lets the legend on the right be properly renderedcreate.barplot: Added ability to create horizontal
barplots - ‘plot.horizontal’, ‘xlimits’, and ‘xat’ parameters added
& examplecreate.scatterplot: Fixing example to adjust placement
of yaxis titlecreate.dotmap: Adding parameter ‘fill.colour’ to allow
user to fill background of cellscreate.barplot: Added ability to draw vertical
linescreate.multiplot: ## Changedd documentation to show to
remove tick markscreate.heatmap: Added check for ## Changedcreate.polygon: Reverted functionality back to using if
statements instead of ternary operatorscreate.heatmap: Added covariate bar between heatmap and
xaxis labelscreate.dotmap: Added ‘grid.col.lwd’ and ‘grid.row.lwd’
to allow different weights of gridlinescreate.dotmap: ## Changedd ‘key.left’, ‘key.right’,
‘key.bottom’ to default to 1 so that legends/keys are properly
incorporatedcreate.dotmap: Added example using covariate bar and
legendcreate.heatmap: Use grobPack() fontfamily specification
to avoid unknown Arial font specificationcreate.dotmap: Changed yaxis label default to not be
bolddraw.keycreate.heatmap: Added ‘legend.layout’,
‘legend.between.col’, and ‘legend.between.row’ parameterscreate.dotmap: ## Changedd to use dotmap colour scheme
by default, fixed palette creation for >3 colour schemescreate.dotmap: Added example with 5-colour
backgroundcreate.heatmap: Added set.seed() call at beginning of
examplescreate.scatterplot: Fixed codoc errorcreate.scatterplot: Changed default curves to use
min/max with na.rm=Tcreate.heatmap: Added parameters ‘covariates.grid.row’,
‘covariates.grid.col’, ‘covariates.grid.border’,
‘covariates.top.grid.row’, ‘covariates.top.grid.col’,
‘covariates.top.grid.border’, ‘legend.border’,
‘legend.border.padding’create.heatmap: Added parameters ‘covariates.padding’,
and ‘covariates.top.padding’ to allow for empty space between covariate
bars and dendrogramscreate.heatmap: Changed ‘grid.row’ and ‘grid.col’ to
default to falsecreate.heatmap: No longer assumes that matrices with
less than 125 rows/columns should have grid linescreate.heatmap: Added code to close devices opened by
the grid::covertUnit function and remove Rplots.pdf files if
necessarydraw.keycreate.dendrogram: Interface change - renamed
cluster.dimensions (pl.) to cluster.dimension (s.) because only takes
scalarscreate.dendrogram: Code clean-upcreate.dendrogram: Fixed handling of jaccard
distancecreate.segplot: ## Removed warning caused by typo in
man filedraw.key()create.densityplot: Set groups to an ordered factor
(avoids auto-alphabetical ordering by lattice during plotting)create.polygon: Added examplecreate.segplot: ## Removed unused parameter from
function definition & fixed inconsistenciescreate.boxplot: Replaced call to panel.BL.bwplot with
call to panel.bwplotcreate.dotmap: ## Changedd example to use new dotmap
colour scheme from default.colourscreate.segplot: Added new function to create
segplotscreate.heatmap: Added notes in help file for using
euclidean when lots of ties and correlation failscreate.violinplot: Fixed a ## Fixed in extra points
argumentcreate.scatterplot: Added alpha argument to control
plotting transparencycreate.dendrogram: ## Changedd to use dist(method =
“jaccard”) instead of jaccard.distance()create.polygon: Fixed border.col argument to allow
different coloured borders for multiple groupscreate.dendrogram: Changed jaccard.distance to use
‘t(x)’ instead of ‘x’ in order to imitate behaviour of dist
functioncreate.polygon: New arguments ‘extra.points’,
‘extra.points.cex’, ‘extra.points.col’, to allow for points plotted on
top of main plotcreate.polygon: New arguments ‘xgrid.at’, ‘ygrid.at’,
‘grid.col’ to allow for grid lines in the background of the main
plotcreate.violin.plot: New arguments ‘extra.points’,
‘extra.points.cex’, ‘extra.points.col’, to allow for points plotted on
top of main plotcreate.violin.plot: New arguments ‘fill.colour’,
‘border.lwd’ to allow for control of interior colours and exterior
border widthscreate.scatterplot.with.error: New arguments
‘strip.col’, ‘strip.cex’ to control size and background colour of panel
labelscreate.scatterplot.with.error: New argument
‘error.bar.length’ to adjust size of error bar whiskerscreate.stripplot: Added parameters for groups, layout,
padding around graph, key and legend, and example for how to use
‘groups’ parametercreate.barplot: Added example using covariates with
labels/covariate legendcreate.scatterplot: Added example using covariates with
labels/covariate legendcreate.heatmap: Resolved codoc mismatch introduced in
v3.2.19create.heatmap: Replaced arguments ‘border’ and
‘border.lwd’ with ‘grid.colour’ and ‘grid.lwd’create.heatmap: Added ability to turn off interior
gridlines using ‘grid.row=FALSE’, ‘grid.col=FALSE’ or ‘grid.lwd=0’create.dendrogram: ## Changedd to use jaccard.distance
instead of vegdistcreate.survival.plot from 2000 to 100create.histogram: Added support for horizontal and
vertical ablinecreate.heatmap: Added ‘text.col’ parametercreate.heatmap: Added example of using unicode symbols
instead of text - similar to dotmap, but allows clusteringcreate.heatmap: Correct ordering of text in clustered
datacreate.scatterplot: Reordered ‘legend’ and
‘layout.width’ arguments to fix padding issuescreate.scatterplot.with.error: Reordered ‘legend’ and
‘layout.width’ arguments to fix padding issuescreate.stripplot: Added ‘jitter’ argument to allow for
staggering of data along x-axiscreate.histogram: Added parameters for padding,
spacing, layout, panelcreate.histogram: Specifying type = “cairo” for all
tiff() calls in Rd files - needed for building package on Maccreate.multiplot: Specifying type = “cairo” for all
tiff() calls in Rd files - needed for building package on Maccreate.scatterplot: Added option ‘abline.v’ to draw
vertical linescreate.densityplot: Fixed ## Fixed when grids are added
- now if type=c(“g”,“l”), xyplot.panels do not double call “g” circle
symbols instead of linescreate.multiple.boxplots: ## Changedd x-axis
label/rotation variable names to match other plotting functions &
added argument to allow for specification of main.cexcreate.stripplot: ## Changedd x-axis rotation variable
name to match other plotting functions & added arguments to specify
x/ylab.col, x/yaxis.col/tck/rotcreate.violinplot: ## Changedd x-axis label/rotation
variable names to match other plotting functions & added arguments
to allow for specification of x/ylab.col, x/yaxis.col/tck/rotcreate.histogram: Added arguments to allow for
specification of x/yaxis.col/tck, x/ylab.col, x/yaxis.rotcreate.polygon: Added arguments to allow for
specification of x/yaxis.col/tck, x/ylab.col, x/yaxis.rotcreate.qqplot.comparison: Added arguments to allow for
specification of x/yaxis.col/tck, x/ylab.colcreate.qqplot.fit: Added arguments to allow for
specification of x/yaxis.col/tck, x/ylab.colcreate.scatterplot: Added arguments to allow for
specification of x/yaxis.col/tck, x/ylab.colcreate.scatterplot.with.error: Added arguments to allow
for specification of x/yaxis.col/tck, x/ylab.colcreate.barplot: Added example with covariatescreate.multiplot: Adjusted formatting and ## Removed
de## Fixedging codecreate.scatterplot: Added option ‘abline.v’ to draw
vertical linescreate.heatmap: ## Changedd x/y label variable names to
match other plotting functions, and added arguments to allow for
specification of ‘yaxis.rot’, ‘xaxis.col’, ‘yaxis.col’, ‘xlab.col’,
‘ylab.col’, ’main.cexcreate.hexbinplot: ## Changedd x/y label variable names
to match other plotting functions, and added arguments to allow for
specification of ‘yaxis.rot’, ‘xaxis.col’, ‘yaxis.col’, ‘xlab.col’,
‘ylab.col’, ‘xaxis.tck’, ‘yaxis.tck’create.dotmap: ## Changedd x/y label and x/y cex
variable names to match other plotting functions, and added arguments to
allow for specification of ‘yaxis.rot’, ‘xaxis.col’, ‘yaxis.col’,
‘xlab.col’, ‘ylab.col’create.multiplot: Clarified labels on 6 panel
examplecreate.barplot: ## Changedd examples to use new
variablescreate.densityplot: ## Changedd examples to include new
variablescreate.multiplot: Added example with 6 panels &
modified variable names to be consistentcreate.barplot: Changed x/yaxis label variable names,
## Changedd to accept arguments for x/yaxis rotation, x/y axis label and
tick label colour, and length of x/y axis tick markscreate.barplot.with.error: Changed x/yaxis label
variable names, ## Changedd to accept arguments for x/yaxis rotation,
x/y axis label and tick label colour, and length of x/y axis tick
markscreate.boxplot: Changed x/yaxis label variable names,
## Changedd to accept arguments for x/yaxis rotation, x/y axis label and
tick label colour, and length of x/y axis tick markscreate.densityplot: Changed x/yaxis label variable
names, ## Changedd to accept arguments for x/yaxis rotation, x/y axis
label and tick label colour, and length of x/y axis tick markscreate.stripplot: Implemented customizable character
colourcreate.multiple.stripplots: Implemented customizable
character colourcreate.multiplot: Improved consistency of test output
file names and variable namescreate.densityplot: Changed defaults to not display
axis linescreate.hexbinplot: Changed defaults to not display axis
linescreate.scatterplot.with.error: Changed defaults to not
display axis linescreate.dotmap: Added ‘xaxis.lab.cex’ and
‘yaxis.lab.cex’ parameters to specify size of axis labelscreate.dotmap: Added ‘key.top’ parameter to specify
size of space between colourkey and xaxis.labelcreate.heatmap: Added ‘axes.lwd’ parameter to change
border widthcreate.multiplot: Added example combining a stripplot
and heatmapcreate.heatmap: Added ‘xat’ and ‘yat’ parameters to
specify label locationscreate.scatterplot: Added horizontal abline parameter -
able to specify line width and typecreate.dendrogram: Added ‘jaccard’ option for
calculating distance (for clustering discrete variables)create.heatmap: Added ‘jaccard’ option for calculating
distance (for clustering discrete variables)create.heatmap: Added example using covariate
legendcreate.heatmap: ## Changedd parameter for cell text
font size & clarified definitions of ‘row.lines’ and
‘col.lines’create.heatmap: Added parameters to control text in
cells and to manually specify row/column grid vectorscreate.multiplot: Improved legend functionalitycreate.heatmap: Added ability to insert text in cells
& added examplecreate.heatmap: Added parameters ‘title.just’ and
‘title.fontface’ to customize legend titlescreate.heatmap: Edited documentation to finalize
examplescreate.multiplot: Added parameters for more
customization - ‘main.cex’, ‘xlab.cex’, ‘ylab.cex’, ‘xlimits’,
‘ylimits’create.dendrogram: Added ‘jaccard’ option for
calculating distance (for clustering discrete variables)create.heatmap: Added ‘jaccard’ option for calculating
distance (for clustering discrete variables)create.heatmap: Added example using covariate
legendcreate.heatmap: ## Changedd examples to be fewer and
follow a logical progressioncreate.hexbinplot: Altered layout.widths to
automatically adjust key.right if colourkey is added (previously
right.padding was adjusted and legend was occasionally cut off)create.heatmap: Added ability to take more than three
colourscreate.heatmap: Added parameters ‘shrink’, ‘border’,
‘border.lwd’create.multiplot: ## Changedd example to use
create.heatmap instead of base lattice::levelplotcreate.heatmap: Added parameter ‘force.clustering’ to
allow user to ignore the row-limitationcreate.dendrogram: Added parameter ‘force.clustering’
to allow user to ignore the row-limitationcreate.histogram: ## Removed check of ‘x’ to ensure it
is a formula - problematic is function is called within another
functioncreate.multiplot: Changing default of
‘xaxis.alternating’ parametercreate.multiplot: Added ‘panel.widths’ parameter &
an example to the documentationcreate.multiplot: ## Removed internal axes labels in
cases where plot axes are identicalcreate.scatterplot: Fixed file formatting to use
tabscreate.multiplot: Fixed file formatting to use tabs
instead of spacescreate.multiplot: Changed name of example outputcreate.heatmap: Changed default colour scheme to use
two colours if data is one-sided and three colours if data is
two-sidedcreate.heatmap: ## Changedd documentation to link to
related man pagescreate.heatmap: Added parameters ‘covariate.legends’,
‘legend.cex’, ‘legend.title.cex’, and ‘legend.side’ to allow users to
include a legend for the covariatescreate.plot.with.levelplot
to create.multiplotcreate.histogram: Added ‘x’ parameter to take in
formulas, leaving ‘data’ parameter to take in datacreate.multiplot: Renamed this function - previously
called ‘create.plot.with.levelplot’create.multiplot: ## Changedd to take any number of
plots and display them in the specified layoutcreate.multiplot: Replaced parameters ‘plot.object’ and
‘levelplot.object’ with ’plot.objectscreate.multiplot: Replaced parameter ‘spacing’ with
‘yspacing’create.multiplot: Added parameters ‘xspacing’ and
‘plot.layout’create.barplot: Added parameter ‘border.col’ to control
border colourcreate.barplot: Added parameters ‘abline.h’,
‘abline.type’, ‘abline.lwd’, ‘abline.col’ to add superimposed linecreate.boxplot: Added parameters ‘abline.h’,
‘abline.type’, ‘abline.lwd’, ‘abline.col’ to add superimposed linecreate.barplot: Added ‘panel.abline’create.boxplot: Added ‘panel.abline’create.heatmap: Added parameters ‘xlab’, ‘ylab’ and
ability to place x-axis label on top axiscreate.plot.with.levelplot: Added error checking for
trellis objectscreate.heatmap: Added ability to plot covariates
without dendrogramscreate.heatmap: Added parameters ‘row.dendrogram’ and
‘col.dendrogram’ to allow users to pass in dendrogramscreate.dendrogram() and
covariates.grob()create.plot.with.levelplot: ## Changedd border
examplecreate.plot.with.levelplot: Improved ability to control
axis labelscreate.plot.with.levelplot: Added padding
parameterscreate.scatterplot: ## Changedd to allow for parameters
of length one specify properties of all curves with ‘add.curves’
optioncreate.scatterplot: Added warning for cases when curves
are drawn with data containing groups where grouping variables are being
## Removedcreate.plot.with.levelplot: Reformatted example
codecreate.plot.with.levelplot: Improved readability of
parameter listcreate.scatterplot: ## Changedd panel.curve code to
avoid ‘no visible binding for global variable x’ errorcreate.scatterplot.with.error: Minor formatting fix to
examplecreate.scatterplot: Added parameter ‘key.top’ to
control spacing above the keycreate.heatmap: Renamed parameter ‘data.to.cluster’
with ‘x’create.heatmap: Cleaned up code by removing spurious
print statementscreate.dotmap: Changed default colour schemecreate.heatmap: Renamed parameters ‘names.row’ and
‘names.col’ with ‘xaxis.lab’ and ‘yaxis.lab’create.heatmap: Added new parameter ‘xaxis.col’ to set
colours of axis labelscreate.heatmap: Cleaned up code by standardizing
variable names and adjusting error-handlingcreate.heatmap: Cleaned up codecreate.heatmap: Added example of how to specify row and
column labelscreate.scatterplot: Changed formatting to produce a
smaller gap between title and plotcreate.scatterplot: ## Changedd example to include
legend and filenamecreate.scatterplot: Cleaned up code by removing
inverted linecreate.scatterplot: Added example to draw colour depth
to scatterpointscreate.scatterplot: Fixed ## Fixed in default behaviour
for ‘curve.from’ and ‘curve.to’ parameterscreate.scatterplot: ## Changedd examplecreate.scatterplot: Cleaned up codecreate.scatterplot: Replace parameter ‘add.lines’ with
‘add.curves’, this allowing the user to draw any segment of any curve
that can be specified with a functioncreate.scatterplot: Added example to demonstrate use of
‘add.curves’ parametercreate.polygon: Fixed ‘alternating’ parameter to force
x-axis labels to be on the bottom rowcreate.polygon: ## Changedd examplecreate.polygon: ## Changedd ‘top.padding’ and
‘bottom.padding’ parameterscreate.scatterplot: Added ability to draw line segments
on plotting regioncreate.violin.plot: ## Changedd to allow boundaries and
scalingcreate.plot.with.levelplot: Added this function by
merging ‘create.boxplot.with.levelplot’ and
‘create.scatterplot.with.levelplot’create.scatterplot.with.levelplot: Added this
functioncreate.heatmap: Added parameters to support ?dist based
distance measures for clusteringcreate.hexbinplot: Added warning if specified ‘maxcnt’
is less than the actual max countcreate.boxplot: ## Changedd to force axis labels to
always be on the left or bottomcreate.qqplot.comparison: Added option of choosing
difference methods to draw a reference linecreate.qqplot.fit: Added option of choosing difference
methods to draw a reference linecreate.qqplot.fit: Added ability to draw confidence
bands for grouped datacreate.dotmap: Standardized parameter namescreate.dotmap: Added example of using
‘padding.text’create.qqplot.fit: Added polygon plots for confidence
intervalscreate.scatterplot: Fixed ‘add.axes’ parameter default
value in documentationcreate.scatterplot: Changed default value of ‘add.axes’
parameter to FALSEcreate.polygon: Added ‘use.loess.median’ and
‘use.loess.border’ parameterscreate.barplot: Added parameters to change colour and
font size of the panel titlecreate.boxplot: Added parameters to change colour and
font size of the panel titlecreate.polygon: Added parameters to change colour and
font size of the panel titlecreate.scatterplot: Added parameters to change colour
and font size of the panel titlecreate.hexbinplot: ## Removed appearance of artificial
blue dot at origincreate.qqplot.fit: Changes to ensure expected
functionalitycreate.qqplot.fit: Deleted function ‘single.qqplot.CI’
and revised corresponding part in function
‘create.qqplot.fit’create.histogram: Changed formatting of
documentationcreate.multiple.stripplots: Added ‘ylab.axis.padding’
parametercreate.heatmap: Changed to set default font sizes from
lookup file (based on size of input)create.polygon: Cleaned up codecreate.multiple.boxplots: Added ‘ylab.axis.padding’ and
‘ylab.cex’ parameterscreate.dotmap: Changed default grid line colour to grey
when no background colour is presentcreate.qqplot.comparison: Fixed examplescreate.qqplot.comparison: Fixed examplescreate.qqplot.comparison: Added functionality of
drawing confidence bandscreate.qqplot.comparison: Changed label default
behaviourcreate.qqplot.fit: Changed label default behaviourcreate.dotmap: Changed default grid line colour to
black if background colour is presentcreate.polygon: Fixed grouping functionality and
examplecreate.polygon: Added translucent colourscreate.polygon: Changed input parameter settings to be
more intuitivecreate.polygon: Added examples (including grouping
example)create.scatterplot: ## Removed redundancy in code by
parameterizing y=x line, and changed examplecreate.boxplot.with.levelplot: Added more examplescreate.qqplot.fit: Improvements to code formattingcreate.qqplot.comparison: Improvements to code
formattingcreate.hexbinplot: Added ‘xaxis.labels’ and
‘yaxis.labels’ parameterscreate.boxplot.with.levelplot: Improved examplecreate.barplot: Added panel parameterscreate.scatterplot: Added panel parameters and improved
input method of ‘groups’ parametercreate.polygon: Cleaned up example namescreate.scatterplot: Added ‘layout’ and ‘xaxis.tck’
parameters to specify figure arrangement and length of tick markscreate.scatterplot: Added example to show lines
connecting dots to the x-axiscreate.qqplot.fit: Added examplecreate.qqplot.comparison: Renamed from
‘create.qqplot2’ functioncreate.qqplot.fit: Renamed from
‘create.qqplot’ functioncreate.scatterplot: ## Changedd example output names
for consistencycreate.qqplot: Code-reviewcreate.qqplot2: Code-reviewcreate.qqplot: ## Changedd code and documentationcreate.qqplot2: ## Changedd code and documentationcreate.qqplot2: Added function to create two-sample qq
plotscreate.qqplot: Added function to create one-sample qq
plotscreate.boxplot.with.levelplot: ## Changedd
documentationcreate.polygon: ## Changedd documentationcreate.heatmap: Added ‘print.color.key’ parameter to
enable turning “off” of colourkey printingcreate.boxplot.with.levelplot: Added new functioncreate.polygon: Added new functioncreate.violin.plot: ## Changedd examplescreate.dotmap: ## Changedd documentationcreate.boxplot: Added ‘x.tck’ parameter to control
length of tick markscreate.dotmap: Added new plotting functioncreate.boxplot: Added panel parameterscreate.heatmap: Added ‘x.alternating’ parameter to
control position of x-axis labelscreate.multiple.stripplots: Added ‘type’ parameter to
allow users to change the type of plotting characterscreate.heatmap: Added ‘xlab’ and ‘ylab’ parameterscreate.heatmap: Added functionality of removing column
and/or row grid-linescreate.multiple.stripplots: Added new plotting function
to create multiple stripplotscreate.multiple.boxplots: Added ‘header.cex’ parameter
to control font size of the headercreate.violin.plot: Added ‘xaxis.labels’ and
‘yaxis.labels’ parameters to control axes labellingcreate.heatmap: Added ‘top.padding’ and
‘bottom.padding’ parameters to control top and bottom marginscreate.histogram: Added ‘lwd’ and ‘lty’ parameters to
control line width and line stylecreate.histogram: Fixed code to work without axes
labelscreate.scatterplot: Added ‘lty’ parameter to control
line style and adjusted examplecreate.scatterplot.with.error: Added ‘lty’ parameter
and adjusted examplecreate.boxplot: Reverted functionality to use
panel.BL.bwplotcreate.scatterplot: ## Changedd examplescreate.histogram: ## Changedd examplescreate.scatterplot.with.error: ## Changedd
examplescreate.violinplot: ## Changedd examplescreate.heatmap: Added ‘right.padding’ and
‘left.padding’ parameters to control marginscreate.hexbinplot: Cleaned code and fixed links in
documentationcreate.hexbinplot: Changed implementation to address
critical issues related to ‘maxcnt’ argumentcreate.hexbinplot: ## Changedd documentation with links
and examplecreate.barplot: ## Changedd examplecreate.densityplot: ## Changedd examplecreate.hexbinplot: Development version - ## Fixed
related to ‘maxcnt’ parametercreate.hexbinplot: Added ‘grid’ and ‘abline’ parameters
and corresponding examplecreate.hexbinplot: Added ‘colorcut’, ‘mincnt’, ‘maxcnt’
parameters to allow user to specify number of bins in plotcreate.hexbinplot: Added ‘aspect’ parameter to adjust
plot sizecreate.hexbinplot: Added ‘xaxis.cex’ and ‘yaxis.cex’
parameterscreate.boxplot: ## Changedd code to remove unnecessary
dependenciescreate.boxplot: Added ‘fill’ parameter to control the
fill colour and corresponding examplecreate.scatterplot: ## Changeds to the examplescreate.dotmap: Reintroduced ‘key’ parameter into
functioncreate.dotmap: Added ‘legend’ parameter to allow for
multiple keyscreate.scatterplot: ## Changedd functionality to allow
for log-scale x- and y-axescreate.scatterplot: Cleaned up documentationcreate.densityplot: Added ‘xaxis.labels’ and
‘yaxis.labels’ parameterscreate.violin.plot: Added example using legendcreate.scatterplot.with.error: Added example using
legendcreate.scatterplot: ## Changedd examplecreate.hexbinplot: Added example using legendcreate.histogram: Added example using legendcreate.boxplot: Added example using legendcreate.densityplot: Added example using legendcreate.barplot.with.error: Added example using
legendcreate.barplot: Added example using legendcreate.barplot.with.error: ## Changedd examplecreate.dotmap: ## Removed ‘legend’ parametercreate.scatterplot: ## Changedd example filenamescreate.scatterplot: Added example using legendcreate.barplot.with.error: Cleaned up codecreate.densityplot: ## Changedd code to use a single
panel functioncreate.heatmap: ## Changedd examples to be sequential
and added example using covariatescreate.scatterplot: Added ‘abline’ argumentcreate.scatterplot.with.error: Added ‘abline’
argumentcreate.scatterplot: Added ability to add multiple keys
to a single plotcreate.scatterplot: Cleaned up code to use a single
panel functioncreate.scatterplot.with.error: Cleaned up code to use a
single panel functioncreate.scatterplot.with.error: ## Changedd formatting
to use tabs instead of spacescreate.scatterplot.with.error: Cleaned up documentation
and examplescreate.scatterplot.with.error: Fixed ## Fixed that
prevented keys from being plottedcreate.densityplot: Changed ‘xat’ and ‘yat’ parameters
into ‘xgrid.at’ and ‘ygrid.at’ parameters to specify grid lines and
added examplecreate.scatterplot: Changed ‘xat’ and ‘yat’ parameters
into ‘xgrid.at’ and ‘ygrid.at’ parameters to specify grid lines and
added examplecreate.scatterplot.with.error: Changed ‘xat’ and ‘yat’
parameters into ‘xgrid.at’ and ‘ygrid.at’ parameters to specify grid
lines and added examplecreate.scatterplot: Added example using a legendcreate.barplot: ## Changedd to allow use of
non-factorial variables for groupingcreate.scatterplot.with.error: Fixed error related to
gridcreate.scatterplot: Fixed error related to ‘ylimits’
and ‘xlimits’, ‘yat’ and ’xatcreate.scatterplot.with.error: Fixed error related to
grouped line graphscreate.barplot: Changed to prevent spurious warnings
when specifying colours with ungrouped datacreate.heatmap: ## Changedd examplescreate.heatmap: Cleaned up code to remove deprecated
parameter ‘colour.number.tweak’create.scatterplot: Cleaned up examples to all use the
same datasetcreate.scatterplot.with.error: Cleaned up code to match
documentationcreate.densityplot: Addressed problem of grid drawing
and tick mark locations not lining up when both are required - this
achieved by removing default grid lines and redrawing them using
panel.abline() at user-specified locationscreate.dotmap: ## Changedd default value of ‘xaxis.lab’
and ‘yaxis.lab’ to NULL in order to accept expressionscreate.barplot: ## Changedd documentation and examples
to use more complex datasets and demonstrate use of ‘ylim’ and ‘yat’
parameterscreate.barplot: Added ‘key’ parametercreate.barplot: Changed ‘groups’ parameter to accept an
expression or variablecreate.barplot: Added filename to stacked barplot
examplescreate.barplot: Fixed problem with groupscreate.barplot.with.error: Fixed problem with
groupscreate.barplot: Added user-control for colour picking
for groupscreate.barplot.with.error: Added user-control for
colour picking for groupscreate.barplot: Added ‘group’ and ‘stack’
parameterscreate.scatterplot: Added ability to rotate text in
axis labelscreate.scatterplot.with.error: Added group-specific
error bar colour handling under no conditioningcreate.scatterplot.with.error: Added ‘add.axes’
parametercreate.scatterplot.with.error: Added ability to handle
grouped datacreate.scatterplot: Added ‘xaxis.labels’ and
‘yaxis.labels’ parameter to allow customization of axis labelscreate.dotmap: ## Changedd examplescreate.scatterplot: Added ability to handle grouped
datacreate.heatmap: ## Changedd colouring functionality to
reduce possibility of errorcreate.histogram: Added functionality of colouring
barscreate.hexbinplot: Added functionality of specifying
label sizescreate.boxplot: Added ‘lwd’ parameter to support
production of smaller imagescreate.boxplot: ## Changedd to facilitate horizontal
boxplots annotations for x-axiscreate.barplot.with.error: Changed default line width
of bar outline to match line width of error barcreate.barplot: ## Changedd layout of figure to match
other plotting functionscreate.multiple.boxplots: Reordered parameters to be
consisting with other plotting functionscreate.multiple.boxplots: Added ‘symbol.cex’ parameter
to control size of boxplot dotscreate.boxplot: Fixed so that ‘ylimits’ argument is no
longer silently ignoredcreate.violin.plot: ## Changedd documentation to
clarify circumstances when ‘x’ will be coerced to a factor or shingle
(when horizontal argument set to FALSE)create.hexbinplot: Added ‘compression’ and ‘add.axes’
parameterscreate.multiple.boxplots: ## Changedd ‘right.padding’
to be set to 2create.barplot.with.error: Renamed function from
create.barplot.with.error.r into
create.barplot.with.error.Rcreate.barplot: Fixed ## Fixed that prevented implicit
grouping from workingcreate.barplot.with.error: Fixed ## Fixed that
prevented implicit grouping from workingcreate.scatterplot.with.error: Fixed ## Fixed that
prevented implicit grouping from workingcreate.scatterplot: Fixed ## Fixed that prevented
implicit grouping from workingcreate.barplot.with.error: Added function to create
barplots with customizable error barscreate.violinplot: Added ‘horizontal’ parameter to
allow user to specify whether to plot horizontally or verticallycreate.scatterplot.with.error: Added ‘y.error.up’,
‘y.error.down’, ‘x.error.right’, ‘x.error.left’ parameter to allow for
drawing horizontal and/or vertical error bars (## Removed ‘error.plus’
and ‘error.minus’ parameters)create.scatterplot.with.error: Added ‘x.error.bar.col’
and ‘y.error.bar.col’ parameterscreate.scatterplot.with.error: Added
‘error.whisker.angle’ parameter to control the angle of whiskers drawn
at both ends of the error barscreate.boxplot: Added ‘xaxis.labels’ parametercreate.heatmap: Added ‘cor.method’ parametercreate.barplot: ## Changedd default to give x-axis and
y-axis scale labelscreate.heatmap: Renamed ‘legend.cex’ parameter to
‘colorkey.cex’create.heatmap: Fixed functionality of ‘colour.alpha’
parametercreate.heatmap: Added example to demonstrate usage of
‘colour.alpha’ parametercreate.scatterplot.with.error: Added function to create
scatterplot with error bars overlaidcreate.barplot: Added ‘yaxis.labels’ parametercreate.scatterplot: Changed panel function to allow for
## Changed() to change conditioned trellis objectcreate.multiple.boxplots: Changed c() to stack() to
accommodate data.framescreate.violin.plot: ## Changedd to match other plotting
functionscreate.barplot: Added ‘col’ parameter to control the
fill colour of barscreate.scatterplot: Added default values for some
parameterscreate.stripplot: Added default values for some
parameterscreate.violinplot: Added default values for some
parameterscreate.barplot: Renamed parameters to standardize with
other plotting functionscreate.multiple.boxplots: Renamed parameters to
standardize with other plotting functionscreate.heatmap: Added verbose warning when function
cannot generate a figurecreate.boxplot: Fixed broken default handling of y-axis
scale labelscreate.heatmap: Fixed ## Fixed to accept NAs when
specifying colour-rangescreate.barplot: Changed ‘xlab’ and ‘ylab’ parameters
into ‘xlab.label’ and ‘ylab.label’ and reordered parameterscreate.boxplot: Changed ‘xlabel’, ‘ylabel’,
‘xlabel.cex’, and ‘ylabel.cex’ parameters into ‘xlab.lab’, ‘ylab.lab’,
‘xlab.cex’, ‘ylab.cex’ and reordered parameterscreate.hexbinplot: Changed ‘xlabel’, ‘ylabel’
parameters into ‘xlab.label’, ‘ylab.label’create.stripplot: Changed ‘xlabel’, ‘ylabel’,
‘xlabel.cex’, ‘ylabel.cex’ into ‘xlab.lab’, ‘ylab.lab’, ‘xlab.cex’,
‘ylab.cex’ and reordered parameterscreate.violinplot: Changed ‘ylabel’ parameter into
‘ylab.label’create.histogram: Adjusted examplecreate.multiple.boxplots: Adjusted examplecreate.scatterplot: Renamed ‘xlabel’, ‘ylabel’,
‘xlabel.cex’, ‘ylabel.cex’ parameters to ‘xlab.label’, ‘ylab.label’,
‘xlab.cex’, ‘ylab.cex’create.histogram: Changed default to plot percentages
instead of densitiescreate.scatterplot: Adjusted example to show extra ##
Changedcreate.densityplot: Added new function to plot
densitiescreate.histogram: Added many new parameters, changed
order of parameters, renamed parameters for standardizationcreate.boxplot: Improved examplecreate.histogram: Improved examplecreate.multiple.boxplots: Fixed spacing/indentation to
match coding standardcreate.histogram: Reordered parameters to have
mandatory parameters come firstcreate.stripplot: Reordered parameters to have
mandatory parameters come firstcreate.violinplot: Reordered parameters to have
mandatory parameters come firstcreate.histogram: Allowed lattice default values for
breaks, ylimits, etccreate.violinplot: Allowed lattice default values for
ylimits, yatcreate.heatmap: Added examples to documentationcreate.heatmap: Fixed but in example by changing
datasetcreate.heatmap: Added ‘colorkey.labels’ parametercreate.boxplot: Renamed parameter ‘ylimit’ to ‘ylimits’
to standardize with other plotting functionscreate.heatmap: Added ‘at’ and ‘colorkey.labels.at’
parameterscreate.heatmap: Enforced graphics type to ‘cairo’ for
all platformscreate.scatterplot: Renamed ‘lwdoutline’ parameter to
‘axis.lwd’ for consistency in parameter namescreate.scatterplot: Added parameters for fontfaces of
x- and y-axis scalescreate.scatterplot: ## Changedd to allow alteration of
more plotting parameters and to match other plotting functionscreate.stripplot: ## Changedd to allow for alteration
of more plotting parameterscreate.boxplot: ## Changedd to allow for alteration of
more plotting parameterscreate.heatmap: Changed default colour.scheme from
legacy parameter-handlingcreate.heatmap: ## Removed spurious warnings in legacy
code and added error-handling for bad usagecreate.scatterplot: Added ‘compression’ parameter for
tiff file customizationcreate.heatmap: Allowed clustering of only one
dimension at a timecreate.scatterplot: Added ‘lwd’ parameter for best-fit
linescreate.heatmap: Changed ordering of top covariates to
match right covariatescreate.heatmap: Changed axis tick-marks to be dynamic
based on number of rows/columns in the heatmapcreate.scatterplot: Allowed for removal of
axis-linescreate.boxplot: Fixed colouring issues that arose when
‘box.colour’ argument was passed as a vectorcreate.heatmap: Added ‘fill.colour’ parameter for
backgroundcreate.heatmap: Allowed specification of arbitrary
colour-combinationscreate.heatmap: Added parameter for covariate-sizecreate.heatmap: Allowed for plotting of arbitrarily
large heatmaps when clustering is turned offcreate.boxplot: ## Removed pass-through
parameterization because it can cause crashes when a fixed parameter is
duplicatedcreate.boxplot: Allowed separate sizing of axis labels
and axis scalescreate.boxplot: Renamed ‘box.color’ to ‘box.colour’ to
match other variablescreate.boxplot: Added ‘symbol.cex’ parameter to adjust
outlier point sizecreate.barplot: Parameterized label-sizescreate.boxplot: Added ‘box.color’ parametercreate.boxplot: ## Changedd to return a handle to plot
object and added default values to input argumentscreate.multiple.boxplots: ## Changedd to get better
memory efficiencycreate.barplot: Adjusted cex parameterscreate.histogram: ## Changedd to allow specification of
type (percent, count, or density)create.heatmap: ## Changedd to allow for adjustment of
colour-rangecreate.heatmap: Added selective plotting of
right/top/left dendrogramscreate.heatmap: Improved colour-palette selection by
calculating the range of the datacreate.heatmap: Allowed specification of main figure
titlecreate.heatmap: Allowed separate output of a file
and/or return of a trellis objectcreate.heatmap: Added BlueWhiteYellow
colour-schemecreate.heatmap: ## Changedd to not run wit an invalid
colour-schemecreate.boxplot: Added option to plot or not plot
outlierscreate.hexbinplot: Added new function to create hexbin
plotscreate.boxplot: ## Changedd to control x- and y-axis
tick sizescreate.heatmap: Added ability to change legend
sizecreate.boxplot: ## Changedd so that x-axis label does
not overlap with x-axis tickscreate.boxplot: ## Changedd to be able to set label
sizecreate.dotmap: Added new function to create
dotmapscreate.scatterplot: Added examplescreate.scatterplot: Added parameters for plot-type,
point/line size, colour, and symbolcreate.barplot: Fixed handling of clustering methods
other than ‘none’ or ‘diana’create.heatmap: Allowed for column-wise covariatescreate.heatmap: Allowed for any agglomerative
clustering method available via hclustcreate.boxplot: Allowed for rotation of x-axis
namescreate.stripplot: Added new function to create strip
plotcreate.barplot: Added new function to create
barplotcreate.boxplot: ## Changedd to save figure directly and
added examplecreate.heatmap: Fixed ## Fixed in parameter-handling
that introduced spurious warningscreate.multiple.boxplots: Modified to remove
build/check warningscreate.multiple.boxplots: Modified to ensure
functionality when ‘plot.names’ input has less components than the
‘data’ inputcreate.multiple.boxplots: Fixed error where called
wrong function name and one argument was missing in create.boxplot: Added new function to create
boxplotscreate.multiple.boxplots: Added new function to create
multiple boxplotscreate.heatmap: Added ability to have clustered data
without dendrogramscreate.heatmap: Added ability to handle different
clustering algorithms and not plot dendrogramscreate.histogram: Added function to create
histogramscreate.scatterplot: Added function to create
scatterplotscreate.heatmap: Added function to create heatmapscreate.violin.plot: Added function to create violin
plots