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Auto axis scaling #165

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Oct 26, 2023
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fa54851
Clean up auto.axis() code style
dan-knight Oct 9, 2023
6cd81eb
Setup existing tests in testthat format
dan-knight Oct 9, 2023
f28d07e
Add deprecation warning for old test format
dan-knight Oct 9, 2023
638096c
Update changelog
dan-knight Oct 9, 2023
c7892cf
Merge branch 'main' into danknight-setup-testthat
dan-knight Oct 9, 2023
f199607
Remove test deprecation warning
dan-knight Oct 9, 2023
798c6ee
Update changelog
dan-knight Oct 9, 2023
e0e1419
Merge branch 'main' of github.com:uclahs-cds/public-R-BoutrosLab-plot…
dan-knight Oct 9, 2023
d688495
Merge branch 'danknight-setup-testthat' of github.com:uclahs-cds/publ…
dan-knight Oct 9, 2023
b48cd31
Axis prep function definition for TDD
dan-knight Oct 9, 2023
2047fde
convert tabs to spaces
forbiddenpersimmon Oct 9, 2023
2c15652
Write function `prep.axis` with default behavior
jsahrmann Oct 9, 2023
05fb146
spelling fixes to comments
forbiddenpersimmon Oct 9, 2023
e4a1bb2
fix line spacing
forbiddenpersimmon Oct 9, 2023
5df60ce
Unit tests for prep.axis
dan-knight Oct 10, 2023
340095a
Fix code style
dan-knight Oct 10, 2023
0c17384
`prep.axis` conditions should use `at`, not `data`
jsahrmann Oct 10, 2023
7f7d4bf
Include input in error message for `prep.axis`
jsahrmann Oct 10, 2023
9623c61
Add parameter `which.arg` to `prep.axis`
jsahrmann Oct 10, 2023
501349c
Use `prep.axis` in `create.boxplot`
jsahrmann Oct 10, 2023
69bef94
Correct data are overwriting in `create.boxplot`
jsahrmann Oct 10, 2023
a20d0bc
Merge branch 'shipit-auto-axis' of github.com:uclahs-cds/public-R-Bou…
forbiddenpersimmon Oct 10, 2023
c8ef633
update auto.axis documentation
forbiddenpersimmon Oct 10, 2023
882b82c
Use `prep.axis` in `create.scatterplot`
jsahrmann Oct 10, 2023
bc9ef47
update parameter documentation for use with
forbiddenpersimmon Oct 10, 2023
9397177
Merge branch 'shipit-auto-axis' of github.com:uclahs-cds/public-R-Bou…
dan-knight Oct 10, 2023
a7831c3
Use `prep.axis` in `create.manhattanplot`
jsahrmann Oct 10, 2023
dca877e
Merge branch 'shipit-auto-axis' of github.com:uclahs-cds/public-R-Bou…
forbiddenpersimmon Oct 10, 2023
b47740b
update parameter documentation for use with
forbiddenpersimmon Oct 10, 2023
31925c1
update parameter documentation for use with
forbiddenpersimmon Oct 10, 2023
9c524bc
Merge branch 'shipit-auto-axis' of github.com:uclahs-cds/public-R-Bou…
forbiddenpersimmon Oct 10, 2023
047ad84
Fix unit tests
dan-knight Oct 10, 2023
370aaac
Remove unnecessary auto.axis message
dan-knight Oct 10, 2023
fc588ea
Merge branch 'shipit-auto-axis' of github.com:uclahs-cds/public-R-Bou…
dan-knight Oct 10, 2023
f35f159
Revert test function removal
dan-knight Oct 10, 2023
62c9e76
Update changelog
dan-knight Oct 10, 2023
8b825a2
Use `prep.axis` in `create.hexbinplot`
jsahrmann Oct 12, 2023
252b1e3
Merge branch 'shipit-auto-axis' of github.com:uclahs-cds/package-Bout…
jsahrmann Oct 12, 2023
9b58b67
update documentation for params associated with
forbiddenpersimmon Oct 16, 2023
6f4e98e
Axis scaling section in vignette
dan-knight Oct 17, 2023
3932063
Add auto axis example plot to vignette
dan-knight Oct 17, 2023
4e26152
Manual axis scaling vignette example plot
dan-knight Oct 17, 2023
7d99e87
Scatterplot auto axis vignette example
dan-knight Oct 18, 2023
7b94705
Merge branch 'shipit-auto-axis' of github.com:uclahs-cds/public-R-Bou…
dan-knight Oct 19, 2023
a260bf1
Log scaled boxplot vignette example
dan-knight Oct 19, 2023
266958c
Log-scaled Manhattan plot vignette example
dan-knight Oct 19, 2023
42f33e5
Log-scaled hexbinplot vignette example
dan-knight Oct 19, 2023
67aa54e
Update changelog
dan-knight Oct 19, 2023
ecaaed2
Fix non-ASCII characters in manual
dan-knight Oct 19, 2023
1c1f827
Update axis scaling manual examples
dan-knight Oct 19, 2023
c34b6e6
Update vignette log scaling examples
dan-knight Oct 20, 2023
9c29136
Vignette log scaling plot refinements
dan-knight Oct 21, 2023
7aaa69d
add self to contributors
forbiddenpersimmon Oct 21, 2023
c578a32
Add self as contributor to DESCRIPTION
jsahrmann Oct 21, 2023
241bfb3
Remove commented code in tests
dan-knight Oct 24, 2023
6148616
Fix author name
dan-knight Oct 24, 2023
9b543a5
Fix docstring
dan-knight Oct 24, 2023
d159687
Merge branch 'shipit-auto-axis' of github.com:uclahs-cds/public-R-Bou…
dan-knight Oct 24, 2023
4c418bf
Update deprecated mockr function
dan-knight Oct 24, 2023
b64523f
Update changelog
dan-knight Oct 24, 2023
7115793
Update Plotting Guide PDF
dan-knight Oct 26, 2023
3424a42
Fix code style in examples
dan-knight Oct 26, 2023
8e798d8
Update changelog
dan-knight Oct 26, 2023
02df664
Fix example code style
dan-knight Oct 26, 2023
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13 changes: 8 additions & 5 deletions DESCRIPTION
Original file line number Diff line number Diff line change
@@ -1,8 +1,8 @@
Package: BoutrosLab.plotting.general
Version: 7.0.10
Version: 7.1.0
Type: Package
Title: Functions to Create Publication-Quality Plots
Date: 2023-10-09
Date: 2023-10-24
Authors@R: c(person("Paul Boutros", role = c("aut", "cre"), email = "PBoutros@mednet.ucla.edu"),
person("Christine P'ng", role = "ctb"),
person("Jeff Green", role = "ctb"),
Expand All @@ -15,18 +15,21 @@ Authors@R: c(person("Paul Boutros", role = c("aut", "cre"), email = "PBoutros@me
person("Caden Bugh", role = "ctb"),
person("Dan Knight", role = "ctb"),
person("Stefan Eng", role = "ctb"),
person("Mohammed Faizal Eeman Mootor", role = "ctb"))
person("Mohammed Faizal Eeman Mootor", role = "ctb"),
person("Rachel Dang", role = "ctb"),
person("John Sahrmann", role = "ctb"))
Maintainer: Paul Boutros <PBoutros@mednet.ucla.edu>
Depends: R (>= 3.5.0), lattice (>= 0.20-35), latticeExtra (>= 0.6-27), cluster (>= 2.0.0), hexbin (>= 1.27.0), grid
Imports: gridExtra, tools, methods, gtable, e1071, MASS(>= 7.3-29)
Suggests:
Suggests:
Cairo (>= 1.5-1),
knitr,
testthat
testthat (>= 3.0.0)
Description: Contains several plotting functions such as barplots, scatterplots, heatmaps, as well as functions to combine plots and assist in the creation of these plots. These functions will give users great ease of use and customization options in broad use for biomedical applications, as well as general purpose plotting. Each of the functions also provides valid default settings to make plotting data more efficient and producing high quality plots with standard colour schemes simpler. All functions within this package are capable of producing plots that are of the quality to be presented in scientific publications and journals. P'ng et al.; BPG: Seamless, automated and interactive visualization of scientific data; BMC Bioinformatics 2019 <doi:10.1186/s12859-019-2610-2>.
License: GPL-2
URL: /~https://github.com/uclahs-cds/package-BoutrosLab-plotting-general
BugReports: /~https://github.com/uclahs-cds/package-BoutrosLab-plotting-general/issues
LazyLoad: yes
LazyData: yes
VignetteBuilder: knitr
Config/testthat/edition: 3
12 changes: 12 additions & 0 deletions NEWS
Original file line number Diff line number Diff line change
@@ -1,3 +1,15 @@
BoutrosLab.plotting.general 7.1.0 2023-10-24

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

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