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BoutrosLab.plotting.general 7.1.1 2024-01-08
UPDATE
* Improved documentation for type parameter in create.scatterplot
* Fix typo in README
--------------------------------------------------------------------------
BoutrosLab.plotting.general 7.1.0 2023-10-26
ADDED
* Add testthat framework for package tests
* Use mockr for unit testing
* Improve documentation for automatic axis scaling in:
- create.scatterplot
- create.boxplot
- create.manhattanplot
- create.hexbinplot
--------------------------------------------------------------------------
BoutrosLab.plotting.general 7.0.10 2023-10-09
UPDATE
* Add deprecation warning for test file in preparation for using
testthat in the v8.0.0 release
--------------------------------------------------------------------------
BoutrosLab.plotting.general 7.0.9 2023-07-21
UPDATE
* Run R CMD check GitHub action weekly and with manual dispatch
* Updated GitHub links to use new "package" prefix
REMOVED
* Remove unnecessary package manual file
--------------------------------------------------------------------------
BoutrosLab.plotting.general 7.0.8 2023-05-26
UPDATE
* Change name of print.to.file() to export.to.file() to avoid naming conflict
with S3 method print()
--------------------------------------------------------------------------
BoutrosLab.plotting.general 7.0.7 2023-05-25
UPDATE
* Expose panel.text arguments for text.above.bar options in create.barplot
* Remove duplicated code in print.multipanel
* Update format of CRAN links
BUG
* Add default label locations for continuous legends
* Fix error with expressions in main for multipanelplots
REMOVED
* Remove outdated plotting data storage code
--------------------------------------------------------------------------
BoutrosLab.plotting.general 7.0.6 2023-02-15
UPDATE
* Move CICD workflow from Dockerhub to GitHub packages
* Add github PR template
UPDATE
* Add text support for create.histogram
UPDATE
* Remove axis labels with axis.lab = NULL in create.boxplot for consistent behavior with other plot types
BUG
* Fix ylab.axis.padding parameter in create.histogram
* Fix error when using expressions in multipanelplot labels and main
--------------------------------------------------------------------------
BoutrosLab.plotting.general 7.0.5 2023-01-03
UPDATE
* Fix typo in man/create.violinplot.Rd
* Add alpha parameter to create.boxplot
* Added GitHub repo to package description
* Correctly sort horizontal barplot
* Remove Makefile
* Replaced string class comparison with is()
BUG
* Fix NEWS format
* Fix bug with persisted plotting function output in examples
--------------------------------------------------------------------------
BoutrosLab.plotting.general 7.0.4 2022-08-17
UPDATE
* Fix border specification in create.polygonplot
--------------------------------------------------------------------------
BoutrosLab.plotting.general 7.0.3 2022-03-15
UPDATE
* Update .Rbuildignore to match lab R standards
--------------------------------------------------------------------------
BoutrosLab.plotting.general 7.0.2 2022-03-07
BUG
* Add type comparisons for class name comparisons
--------------------------------------------------------------------------
BoutrosLab.plotting.general 7.0.1 2022-03-03
BUG
* Fix object protection issue in distance.c
--------------------------------------------------------------------------
BoutrosLab.plotting.general 7.0.0 2022-02-15
UPDATE
* Renamed ks.test.critical.value() function to critical.value.ks.test()
to resolve naming conflict with S3 generic ks.test() from base R stats
package.
BUG
* Fix issue when specifying multiple line-widths in create.polygonplot()
--------------------------------------------------------------------------
BoutrosLab.plotting.general 6.1.0 2021-10-26
UPDATE
* Add option to use dots in a legend instead of default rectangles
* Enable create.boxplot to print different text label on each panel
BUG
* Fixed inconsistent grouping of point colours in create.boxplot
* Account for case where only one colour is passed to create.heatmap
--------------------------------------------------------------------------
BoutrosLab.plotting.general 6.0.3 2021-01-24
UPDATE
* Only use cairo in the examples for covariates.grob and legend.grob
if capabilities('cairo') is true.
--------------------------------------------------------------------------
BoutrosLab.plotting.general 6.0.2 2021-01-04
UPDATE
* Depends versions: R (>= 3.5.0), lattice (>= 0.20-35),
latticeExtra (>= 0.6-27), cluster (>= 2.0.0), hexbin (>= 1.27.0)
* Only use cairo when capabilities('cairo') is true to fix CRAN's issue
of cairo not being available on M1 Macs
--------------------------------------------------------------------------
BoutrosLab.plotting.general 6.0.1 2020-08-05
UPDATE
* Added paper's doi to DESCRIPTION
REMOVED
* Removed use of tocstyle package in PlottingGuide as that is obsolete
and failing CRAN's check
--------------------------------------------------------------------------
BoutrosLab.plotting.general 6.0.0 2020-04-01
UPDATE
* Updated contact email
* Included source code previously imported from BoutrosLab.dist.overload
and BoutrosLab.statistics.general
* Fixed resolutions for examples to reduce running time
* Added \donttest{} to examples that took >5 seconds to run
* Examples now output plots to tempdir()
BUG
* Fixed errors in create.multiplot and create.multipanel that wasn't
passing CRAN's check by changing 'is.na' to 'anyNA'
* Fixed errors in create.multiplot that was only checking the first
element in a list by using 'is.element' instead of '=='
* Fixed spacing issue in PlottingGuide
* Added stringsAsFactors = TRUE to data.frame() calls in examples
(Changes to R-devel in 2020-03-04 changed the defaults)
* Fixed thousands.splits to return a vector instead of a list
* Fixed write.metadata to use double quotes on system calls, correctly
show BL.plotting.survival version and consolidate exiftool calls
to speed things up
* Fixed CRAN error misuse of package= for PACKAGE=
REMOVED
* Removed BoutrosLab.utilities::recode.vector calls in examples
* Removed requirements for BoutrosLab.utilities, BoutrosLab.dist.overload,
BoutrosLab.statistics.general
--------------------------------------------------------------------------
BoutrosLab.plotting.general 5.9.8 2018-10-16
FEATURE
* create.hexbinplot: added option to modify the default legend title
--------------------------------------------------------------------------
BoutrosLab.plotting.general 5.9.7 2018-09-19
BUG
* fixed an issue regarding warning detection for class of conditioning variable that didn't recognize character input (barplot, boxplot, hexbinplot, scatterplot)
--------------------------------------------------------------------------
BoutrosLab.plotting.general 5.9.6 2018-07-24
BUG
* fixed an issue that prevented extra points from plotting correctly in create.polygonplot
--------------------------------------------------------------------------
BoutrosLab.plotting.general 5.9.5 2018-06-05
FEATURE
* added warnings when a formula contains a conditioning variable that is an integer/numeric (barplot, boxplot, hexbinplot, scatterplot)
* changed default xaxis.tck for boxplot to prevent automatic ticks from appearing at top of plot
BUG
* force.colour.scheme no longer requires 'x' when return.scheme = TRUE
* fixed an error in create.scatterplot preventing automatic axis determination when all y == 0 or all y == -N
REMOVED
* removed append.footnote.R as it was non-functional with no plans to fix
--------------------------------------------------------------------------
BoutrosLab.plotting.general 5.9.4 2018-04-18
FEATURE
* dotmap can now do symmetrical removing of top left half of dotmap
BUG
* top covariates in heatmap now have proper defaults
--------------------------------------------------------------------------
BoutrosLab.plotting.general 5.9.3 2018-04-18
FEATURE
* updated dependencies to not include as many
* boxplot now saves all its data (for later use)
* multipanelplot now saves temp plots to temp dir
BUG
* Default.colours no longer references wrong grey scale colour
--------------------------------------------------------------------------
BoutrosLab.plotting.general 5.9.2 2018-04-10
FEATURE
* Legend grob for continous legends now auto place themselves -- x and y pos dont do anything anymore
* Print to file will now override previous entries
* removed printing for individual plot info (too unreliable)
--------------------------------------------------------------------------
BoutrosLab.plotting.general 5.9.1 2018-04-04
FEATURE
* Multipanel plot now uses tob axis labels too for lining up plots
BUG
* Multipanel plot now correctly positions plot main labels
--------------------------------------------------------------------------
BoutrosLab.plotting.general 5.9.0 2018-03-23
FEATURE
* added code for saving data information and trellis object information to each relevant plot
--------------------------------------------------------------------------
BoutrosLab.plotting.general 5.8.16 2018-03-16
FEATURE
* cleaned up the multipanelplot code and updated the examples
--------------------------------------------------------------------------
BoutrosLab.plotting.general 5.8.15 2018-03-13
FEATURE
* made multipanelplot legend/label placement algorithm more optimal
--------------------------------------------------------------------------
BoutrosLab.plotting.general 5.8.14 2018-03-09
FEATURE
* now stores data on the mount
BUG
* text now passed to panel in seperate list, stopping it from being reset in between plots
--------------------------------------------------------------------------
BoutrosLab.plotting.general 5.8.13 2018-02-13
FEATURE
* adjusted polygon plot to work well with roc plot
--------------------------------------------------------------------------
BoutrosLab.plotting.general 5.8.12 2018-02-08
FEATURE
* added lollipop plot as an extension of scatterplot
--------------------------------------------------------------------------
BoutrosLab.plotting.general 5.8.11 2018-02-05
FEATURE
* added ability to disable factor sorting in relative plots
* added example to histogram of type change
BoutrosLab.plotting.general 5.8.10 2018-01-22
FEATURE
* added border colour for histogram bars
--------------------------------------------------------------------------
BoutrosLab.plotting.general 5.8.9 2018-01-12
FEATURE
* added inside legend auto finder code
BUG
* boxplot addstriplot colour was having issue with multiple boxplots, now works properly
--------------------------------------------------------------------------
BoutrosLab.plotting.general 5.8.8 2017-12-19
UPDATE
* updated formatting to match coding standard
* added inside legends to multipanel plot
BUG
* heatmap now accepts both x and y axis covariates
--------------------------------------------------------------------------
BoutrosLab.plotting.general 5.8.7 2017-11-15
UPDATE
* updated formatting to match coding standard
--------------------------------------------------------------------------
BoutrosLab.plotting.general 5.8.6 2017-11-15
FEATURE
* legend and covariate grobs can now use x and y coordinates
BUG
* heatmap using colours must faster
* legacy settings in multipanel plot now affect all individual plots too
--------------------------------------------------------------------------
BoutrosLab.plotting.general 5.8.5 2017-11-01
FEATURE
* force colour scheme now has heteroplasmy fraction and MT annotation
--------------------------------------------------------------------------
BoutrosLab.plotting.general 5.8.4 2017-10-25
BUG FIX
* Multipanel plot now accepts colorkey and draw key legends
* Get defaults now retrieves ArialMT instead of Arial font (actual name on Linux)
FEATURE
* heatmap can now use colours to specify the squares
* density plot can now add text (like bar/boxplot)
--------------------------------------------------------------------------
BoutrosLab.plotting.general 5.8.3 2017-08-11
BUG FIX
* Multipanel plot now works with legends from original plots
* Barplot error bars now work with horizontal plots too
FEATURE
* heatmap now accepts inside legends and can specify text not based on grid cooridnates
--------------------------------------------------------------------------
BoutrosLab.plotting.general 5.8.2 2017-08-11
BUG FIX
* Completely reworked how spacing works in multipanel plot -- now creates rectangular grobs instead of using top/left/right/bottom padding
--------------------------------------------------------------------------
BoutrosLab.plotting.general 5.8.1 2017-08-11
BUG FIX
* Multipanel plot background colour
* Multipanel plot not accepting expression labels
* Multipanel deleting plots main labels
* heatmap legend layout works properly now
--------------------------------------------------------------------------
BoutrosLab.plotting.general 5.8.0 2017-08-11
ADDITIONS
* new create.multiplot function (create.multipanelplot)
BUG FIX
* auto-axis now gives 5 labels by default instead of 4
* same.as.matrix can now be applied to create dendrogram outside of heatmap
* fixed filename error in crete.gif
* heatmap now loads defaults
* segplot defaults to bold like rest of plots
* colours for default dotmap now match the documentation (had to reverse them)
FEATURE UPDATE
*pcawg.colours: new and renamed tumour type names added to palette, sv class 'insertion' assigned colour
--------------------------------------------------------------------------
BoutrosLab.plotting.general 5.7.6 2017-08-11
BUG FIX
* 1D heatmaps now work -- automatically
* Error bars now work properly with grouped bar plots
FEATURES
* automatic layout justification for legends (using just arg) for continous legends
* added helper function for seperating thousands by commas, i.e -> (12345) -> (12,345)
* merged all the relevent colour functions into force.colour.scheme
* can now extract dendrograms from a heatmap (only one, and may require manual manipulation)
--------------------------------------------------------------------------
BUG FIX
* create.heatmap - grid row/column limits reversed
* legend.grob - continuous legends produce warnings
* ytop.rectangle in create.scatterplot() doesn't work properly.
* Remove the old option (retrieve.plot.labels) and merge into (plot.labels.to.retrieve)
FEATURES
* merged multiple colour functions (old ones to be removed in next commit)
* multiple colours of error bars in scatterplot
* Add xaxis.rot.top option to create.multiplot
* have legends on both the left AND the right for create.heatmap
--------------------------------------------------------------------------
BoutrosLab.plotting.general 5.7.4 2017-07-19
BUG FIX
* Automatic labels not working for stacked barplots
* removed log scaling from stacked barplots
* fixed 1 D heatmap issues
ADDITIONS
* search metadata function
--------------------------------------------------------------------------
BoutrosLab.plotting.general 5.7.3 2017-06-06
FEATURE UPDATE
* each plot can put xat/yat = "auto"/"auto.linear"/"auto.log" to get automatic labels
ADDITIONS
* pretty axis function -- input data set gives updated data values and labels
--------------------------------------------------------------------------
BoutrosLab.plotting.general 5.7.2 2017-05-17
FEATURE UPDATE
* Can now add border to correlation keys
* Issues around multiplot reseting labels on y axis when x asis labels added solved
ADDITIONS
* create.gif for creating animated plots
--------------------------------------------------------------------------
BoutrosLab.plotting.general 5.7.1 2017-05-17
BUG FIX
* write.plot.R: fixed an error that didn't allow adding additional plots when returning object to screen (when filename = NULL)
* create.barplot.R: fixed a bug interfering with add.rectangle and removed redundant add.background.shading (repeats add.rectangle functionality)
* force.colour.scheme: if multiple outputs were requested only one would be returned; now returns a list
FEATURE UPDATE
* create.barplot.R: minor improvements to some examples
*split argument lwd into axes.lwd and border.lwd to be consistent with other functions
*removed argument remove.all.border.lines as this can now be accomplished with axes.lwd
MINOR (FORMATTING) CHANGES
* colour.gradient.R, covariates.grob.R, create.barplot.R, create.boxplot.R, create.colourkey.R, create.dendrogram.R, create.densityplot.R,
create.hexbinplot.R, create.segplot.R, create.stripplot.R, create.violinplot.R, default.colours.R, display.colours.R,
display.statistical.result.R, force.colour.scheme.R, generate.at.final.R, get.corr.key.R, get.defaults.R, get.line.breaks.R, legend.grob.R,
scientific.notation.R, show.available.palettes.R, write.metadata.R, write.plot.R:
applied code formatting (BL standards)
--------------------------------------------------------------------------
BoutrosLab.plotting.general 5.7.0 2017-05-11
BUG FIX
* create.violinplot: fixed a bug in colour functionality; now repeats colours when fewer colours are supplied than there are groups
FEATURE UPDATE
* create.hexbinplot: changed argument abline.type to abline.lty to be consistent with other functions
* create.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 functions
MINOR (FORMATTING) CHANGES
* create.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)
--------------------------------------------------------------------------
BoutrosLab.plotting.general 5.6.24 2017-04-20
FEATURE UPDATE
*create.multiplot: Added functionality to add top x-axis tick labels. Has not been extensively tested.
--------------------------------------------------------------------------
BoutrosLab.plotting.general 5.6.23 2017-02-09
BUG FIX
*pcawg.colours: fixed bug that prevented project code colours from being returned.
--------------------------------------------------------------------------
BoutrosLab.plotting.general 5.6.22 2017-02-09
FEATURE UPDATE
*create.dotmap: addition of parameters for rectangle border thickness, rectangle border colour.
--------------------------------------------------------------------------
BoutrosLab.plotting.general 5.6.21 2017-01-30
BUG FIX
* create.scatterplot: adding conditional for when pch is not referring
to a point (this is in reference to KM plots)
--------------------------------------------------------------------------
BoutrosLab.plotting.general 5.6.20 2017-01-28
FEATURE UPDATE
* create.scatterplot: addition of parameter "col.border".
This allows customizable border colours when pch >= 21.
--------------------------------------------------------------------------
BoutrosLab.plotting.general 5.6.19 2016-12-06
FEATURE UPDATE
* pcawg.colours: add project.code to colour.schemes
--------------------------------------------------------------------------
BoutrosLab.plotting.general 5.6.18 2016-11-23
FEATURE UPDATE
* create.polygonplot: option to add rectangles.
--------------------------------------------------------------------------
BoutrosLab.plotting.general 5.6.17 2016-11-08
FEATURE UPDATE
* pcawg.colours: consistent colour palette for use on pcawg data
--------------------------------------------------------------------------
BoutrosLab.plotting.general 5.6.15 2016-10-24
FEATURE UPDATE
* 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 labels
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BoutrosLab.plotting.general 5.6.14 2016-10-05
FEATURE UPDATE
* create.polygonplot: option to add text.
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BoutrosLab.plotting.general 5.6.13 2016-09-28
FEATURE UPDATE
* create.polygonplot: added parameters alpha and median.lwd.
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BoutrosLab.plotting.general 5.6.12 2016-09-07
FEATURE UPDATE
* create.densityplot & create.violinplot: allow adjustment of bandwidth with parameters bandwidth and bandwidth.adjust.
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BoutrosLab.plotting.general 5.6.11 2016-08-31
FEATURE UPDATE
* create.stripplot: allow different border colour for added points when pch >= 21
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BoutrosLab.plotting.general 5.6.10 2016-07-27
BUG FIX
* reintegrated untagged changes to trunk and re-added scatterplot feature updates.
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BoutrosLab.plotting.general 5.6.9 2016-07-25
FEATURE UPDATE
* create.scatterplot: allow different border colour for added points when pch >= 21
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BoutrosLab.plotting.general 5.6.8 2016-05-27
FEATURE UPDATE
* create.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.
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BoutrosLab.plotting.general 5.6.7 2016-05-19
BUG FIX
* create.multiplot: fixed bug where NULL values in parameter list (for xlimits=/ylimits=) were being ignored/unprocessed [BPG-2].
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BoutrosLab.plotting.general 5.6.6 2016-04-29
FEATURE UPDATE
* 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.
BUG FIX
* create.barplot: fixed adding error bars for data-frames [BPG-4]
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BoutrosLab.plotting.general 5.6.5 2016-04-27
MINOR UPDATE
* create.boxplot: Added example for adding text to plot.
* create.hexbinplot: Added example of stratified multiplot.
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BoutrosLab.plotting.general 5.6.4 2016-04-21
FEATURE UPDATE
* create.dotmap: NA plotting character can be made different colours with new variable, NA.spot.size.colour.
Default is set to black.
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BoutrosLab.plotting.general 5.6.2 2016-04-08
FEATURE UPDATE
* get.cor.key: parameterizing number of decimal places to keep for spearman, pearson and kendall correlation values
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BoutrosLab.plotting.general 5.4.3 2016-01-04
BUG FIXES:
* Inconsitency in dotmap/heatmap grid lines location fixed -> everything follows heatmaps spec now
fixed bug where sample.order would reorde barplots incorrectly when horizontal
* default font sizes are consistent now
* default font sizes are more proportional
FEATURE UPDATES:
* ability to add multiple violin fill colours
* able to completely remove borders from heatmaps
* add p values automatically to box plots
* ability to set a sperate set of defaults based on type of publication ( default sets still need to be added)
* ability to pick what plots to retrieve plot labels from in create.multiplot
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BoutrosLab.plotting.general 5.4.2 2015-12-22
FEATURE UPDATE:
* create.scatterplot: added option to specify colour of grid lines.
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BoutrosLab.plotting.general 5.3.9 2015-10-01
FEATURE UPDATE:
* create.heatmap: turns off grid lines when row or column number exceeds a certain threshold.
* auto-removal of grid lines can be overrided with forcing parameters
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BoutrosLab.plotting.general 5.3.7
BUG FIXES:
* same.as.matrix will now correcting readjust label specifications
* when combining scatterplots, they will no longer only use error bars from one scatter plot
* yaxis.covariates parameter can now allow specific location specification so it does not overlap the heatmap
* xgrid.at and ygrid.at now properly update for all functions
* background rectangles are now drawn in the background instead of foreground
* when combining scatterplots, they will no longer only use the text specified from one scatter plot
* removed circular definitions from Rd files
* standardized parameter defaults
FEATURE UPDATES:
* Can now add subtitles through use of xaxis.top parameters
* Can now input a vector of files to be output to
* Can now sort boxes in create.boxplot by max, min, mean and median (defaults to median if not set)
* Can now draw both bands and lines on segplots
* Polygon plot will now auto-calculate x and y limits if not specified
* Can now vertically align labels and adjust there coordinates manually
BoutrosLab.plotting.general 5.3.4 2015-07-31
MINOR UPDATE:
* create.scatterplot: updated ROC example to use auto-label placement
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BoutrosLab.plotting.general 5.3.3 2015-07-28
MINOR UPDATE:
* functions containing the word 'colour' now accept both American and Canadian spelling
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BoutrosLab.plotting.general 5.3.2 2015-07-24
BUG FIXES:
* create.heatmap: fixed bug which made labels disappear when stratifying dendrogram
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BoutrosLab.plotting.general 5.3.1 2015-07-24
MINOR UPDATE:
* minor updates to the plotting guide
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BoutrosLab.plotting.general 5.3.0 2015-07-23
MINOR UPDATE:
* standardized parameter names across all plotting functions
* create.hexbinplot: added add.xyline and add.curves functionality (same as in create.scatterplot)
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BoutrosLab.plotting.general 5.2.20 2015-07-13
MINOR UPDATE:
* 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 components
* default.colours: greyscale check no longer runs if only one colour is requested
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BoutrosLab.plotting.general 5.2.19 2015-07-03
MINOR UPDATE:
* force.colour.scheme: added snv colour scheme
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BoutrosLab.plotting.general 5.2.18 2015-07-03
MINOR UPDATE:
* Standardized all plotting functions to have resolution set to 1600 dpi
* force.colour.scheme: Added spaces in appropriate tissue names
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BoutrosLab.plotting.general 5.2.17 2015-06-16
MINOR UPDATE:
* removed out-of-date comments from examples
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BoutrosLab.plotting.general 5.2.16 2015-06-15
MINOR UPDATE:
* re-created PlottingGuide to use revamped show.available.palettes function
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BoutrosLab.plotting.general 5.2.13 2015-05-08
MINOR UPDATE
* create.multiplot: added example showing how to save parameter options from individual plots
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BoutrosLab.plotting.general 5.2.12 2015-05-07
MINOR UPDATE
* create.heatmap: Added two parameters: text.position and text.offset to customize placement of text in cells
* show.available.palettes: changed display of specific schemes to call create.heatmap (more robust method)
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BoutrosLab.plotting.general 5.2.10 2015-04-22
BUG FIXES
* show.available.palettes: fixed 'general' program to no longer introduces NAs by coersion
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BoutrosLab.plotting.general 5.2.9 2015-04-21
MINOR UPDATE
* create.hexbinplot: added comment to explain maxcnt removing datapoints from example plot
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BoutrosLab.plotting.general 5.2.8 2015-03-12
MINOR UPDATE
* create.barplot: allow vector of custom sorting order for samples
* create.multiplot: has flag to remove all border lines from plots
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BoutrosLab.plotting.general 5.2.6 2014-12-24
MINOR UPDATE
* write.plot: fixed bug
* added new colourkey legend and interface
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BoutrosLab.plotting.general 5.2.5 2014-12-18
MINOR UPDATE
* updated plotting guide to have more examples and slight wording adjustments
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BoutrosLab.plotting.general 5.2.4 2014-12-16
MINOR UPDATE
* create.barplot: ablines now appear in the background of the plot instead of the foreground
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BoutrosLab.plotting.general 5.2.2 2014-12-09
MINOR UPDATE
* write.plot: Added embed.plot functionality (depreciating said function)
* embed.plot: Removed embed.plot()
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BoutrosLab.plotting.general 5.2.1 2014-11-05
MINOR UPDATE
* force.colour.scheme: Bug fix for annovar colour schemes
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BoutrosLab.plotting.general 5.2.0 2014-10-17
MINOR UPDATE
* Added `Nature' style option to all plotting functions
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BoutrosLab.plotting.general 5.1.9 2014-10-16
MINOR UPDATE
* create.scatterplot: for add.line.segments, changed line-end style to 'butt'
* create.stripplot: NEW ARGUMENTS to allow for addition of lines showing group medians
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BoutrosLab.plotting.general 5.1.7 2014-10-10
MINOR UPDATE
* default.colours: added new schemes spiral.noon and spiral.night
* default.colours: rearranged order of qual scheme to decrease red-green combinations
* force.colour.scheme: changed CNV colours to red/blue/green/white, MSI to green/yellow, risk to red/yellow
* reorganized default.colours and force.colour.scheme to return deprecated schemes
* show.available.palettes: reorganized layout of 'specific' scheme output
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BoutrosLab.plotting.general 5.1.6 2014-10-08
MINOR UPDATE
* create.boxplot: added arguments to allow for addition of stripplot in background
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BoutrosLab.plotting.general 5.1.5 2014-09-19
MINOR UPDATE
* show.available.palettes: added new function to show schemes available in default.colours and
force.colour.scheme
* default.colours: refactored, changed greyscale warning to auto-calculate
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BoutrosLab.plotting.general 5.1.4 2014-09-08
MINOR UPDATE
* create.scatterplot: changed argument name - add.lines > add.line.segments
* create.scatterplot: updated to accept lists of line segments to add
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BoutrosLab.plotting.general 5.1.3 2014-08-22
MINOR UPDATE
* PlottingGuide: converting to use knitr, added further details and references to design portion
* MultiPlotTutorial: deleted, contents migrated to PlottingGuide
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BoutrosLab.plotting.general 5.1.2 2014-08-14
MINOR UPDATE
* create.manhattanplot: Updated documentation to use chromosome palette in force.colour.scheme
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BoutrosLab.plotting.general 5.1.1 2014-08-14
MINOR UPDATE
* create.barplot: changed default fill colour to black (instead of grey)
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BoutrosLab.plotting.general 5.1.0 2014-08-12
MINOR UPDATE
* create.scatterplot: NEW ARGUMENTS text.guess.* now allows users to specify data points so that
associated label positions can be automatically determined
* inside.rectangle: NEW FUNCTION which determines if a set of data points are inside a set of defined
rectangles
* inside.ellipse: NEW FUNCTION which determines if a set of data points are inside a set of defined
ellipses
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BoutrosLab.plotting.general 5.0.28 2014-08-08
MINOR UPDATE
* Updated plotting guide to have extended design advice: added sections on resolution, file types, etc
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BoutrosLab.plotting.general 5.0.27 2014-07-31
MINOR UPDATE
* Updated examples in scatterplot, qqplot comparison, hexbinplot, heatmap, dotmap, and barplot to have better formatted axes labels
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BoutrosLab.plotting.general 5.0.26 2014-07-31
BUG FIX
* re-added argument line.lwd in create.scatterplot
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BoutrosLab.plotting.general 5.0.25 2014-07-31
MINOR UPDATE
* create.heatmap: NEW ARGUMENT gridline.order now allows user to specify in which order
gridlines should be drawn (horizontal or vertical first)
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BoutrosLab.plotting.general 5.0.24 2014-07-31
MINOR UPDATE
* adjusted examples in qqplot.comparison, qqplot.fit and scatterplot to use character values for panel groupings
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BoutrosLab.plotting.general 5.0.23 2014-07-30
MINOR UPDATE
* display.colours now additionally displays names of colours
BUG FIX
* added 'eye' to the 'tissue' palette in force.colour.scheme
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BoutrosLab.plotting.general 5.0.22 2014-07-29
MINOR UPDATE
* Fixed: create.scatterplot, add.lines now works with lists of data
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BoutrosLab.plotting.general 5.0.20 2014-07-24
MINOR UPDATE
* Changed multiplot example to use matching gene data
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BoutrosLab.plotting.general 5.0.19 2014-07-23
MINOR UPDATE
* Changing chromosome palette in force.colour.scheme to use more visually distinct colours
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BoutrosLab.plotting.general 5.0.18 2014-07-23
BUG FIX
* Changed datasets keep common genes among datasets
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BoutrosLab.plotting.general 5.0.17 2014-07-21
MINOR UPDATE
* Updated multiplot tutorial with new examples using generate data
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BoutrosLab.plotting.general 5.0.16 2014-07-16
BUG FIX
* default.colours: properly return the requested number of colours when multiple palettes requested
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BoutrosLab.plotting.general 5.0.15 2014-07-11
MINOR UPDATE
* create.scatterplot:
- NEW ARGUMENTs allow for addition of line segments to be drawn
BUG FIX
* get.corr.key: fixed corner definition determined by x.pos and y.pos