Gavin Rhys Lloyd authored on 27/06/2024 13:06:21
| ... | ... |
@@ -33,7 +33,7 @@ M = hca_dendrogram() |
| 33 | 33 |
C = hca_dendrogram() |
| 34 | 34 |
} |
| 35 | 35 |
\references{
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-de Vries A, Ripley BD (2022). \emph{ggdendro: Create Dendrograms and Tree
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-Diagrams Using 'ggplot2'}. R package version 0.1.23, |
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+de Vries A, Ripley BD (2024). \emph{ggdendro: Create Dendrograms and Tree
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+Diagrams Using 'ggplot2'}. R package version 0.2.0, |
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| 38 | 38 |
\url{https://CRAN.R-project.org/package=ggdendro}.
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| 39 | 39 |
} |
- due to changes in struct (removal of unicode)
Gavin Rhys Lloyd authored on 02/02/2024 10:50:50
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@@ -24,7 +24,7 @@ This object makes use of functionality from the following packages:\itemize{ \i
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| 24 | 24 |
\section{Inheritance}{
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A \code{hca_dendrogram} object inherits the following \code{struct} classes: \cr\cr
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-\code{hca_dendrogram()} ⭢ \code{chart()} ⭢ \code{struct_class()}
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+\verb{[hca_dendrogram]} >> \verb{[chart]} >> \verb{[struct_class]}
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} |
| 29 | 29 |
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| 30 | 30 |
\examples{
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- get_description moved to struct and updated
Gavin Rhys Lloyd authored on 31/01/2024 09:48:31
| ... | ... |
@@ -19,9 +19,17 @@ See \code{\link[struct]{chart_plot}} in the \code{struct} package to plot this c
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| 19 | 19 |
A dendrogram visualising the clustering by HCA. |
| 20 | 20 |
} |
| 21 | 21 |
\details{
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-This object makes use of functionality from the following packages:\itemize{\item{\code{ggdendro}}}
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+This object makes use of functionality from the following packages:\itemize{ \item{\code{ggdendro}}}
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| 23 | 23 |
} |
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+\section{Inheritance}{
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+ |
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+A \code{hca_dendrogram} object inherits the following \code{struct} classes: \cr\cr
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+\code{hca_dendrogram()} ⭢ \code{chart()} ⭢ \code{struct_class()}
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+} |
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+ |
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| 24 | 30 |
\examples{
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+M = hca_dendrogram() |
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+ |
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C = hca_dendrogram() |
| 26 | 34 |
} |
| 27 | 35 |
\references{
|
due to roxygen no longer needing % to be escaped.
- add markdown flag to description file
- use text format for citations (includes markdown)
- remove % from descriptions (doesnt work with current implementation)
Gavin Rhys Lloyd authored on 06/07/2023 15:19:12
| ... | ... |
@@ -25,7 +25,7 @@ This object makes use of functionality from the following packages:\itemize{\ite
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| 25 | 25 |
C = hca_dendrogram() |
| 26 | 26 |
} |
| 27 | 27 |
\references{
|
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-de Vries A, Ripley BD (2022). |
|
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-\emph{ggdendro: Create Dendrograms and Tree Diagrams Using 'ggplot2'}.
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-R package version 0.1.23, \url{https://CRAN.R-project.org/package=ggdendro}.
|
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+de Vries A, Ripley BD (2022). \emph{ggdendro: Create Dendrograms and Tree
|
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+Diagrams Using 'ggplot2'}. R package version 0.1.23, |
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+\url{https://CRAN.R-project.org/package=ggdendro}.
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| 31 | 31 |
} |
Gavin Rhys Lloyd authored on 23/01/2023 10:57:52
| ... | ... |
@@ -25,7 +25,7 @@ This object makes use of functionality from the following packages:\itemize{\ite
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C = hca_dendrogram() |
| 26 | 26 |
} |
| 27 | 27 |
\references{
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-de Vries A, Ripley BD (2020). |
|
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+de Vries A, Ripley BD (2022). |
|
| 29 | 29 |
\emph{ggdendro: Create Dendrograms and Tree Diagrams Using 'ggplot2'}.
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-R package version 0.1.22, \url{https://CRAN.R-project.org/package=ggdendro}.
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+R package version 0.1.23, \url{https://CRAN.R-project.org/package=ggdendro}.
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| 31 | 31 |
} |
Gavin Rhys Lloyd authored on 07/07/2021 09:37:19
• GitHub committed on 07/07/2021 09:37:19
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@@ -10,7 +10,10 @@ hca_dendrogram(...) |
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\item{...}{Additional slots and values passed to \code{struct_class}.}
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} |
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\value{
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-A \code{hca_dendrogram} object.
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+A \code{
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+hca_dendrogram |
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+} object. This object has no \code{output} slots.
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+See \code{\link[struct]{chart_plot}} in the \code{struct} package to plot this chart object.
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} |
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\description{
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A dendrogram visualising the clustering by HCA. |
* fix base=10 regardless of input (see #15)
class constructor was always setting base to 10 instead of the input value
* merge bug fix 1.01 into dev (#19)
* bug fix issue #7
Correctly re-order the sample_meta column for colouring samples in the dendrogram plot
* version bump
bug fix issue #7
* fix for https://github.com/computational-metabolomics/structToolbox/issues/18 (#20)
correctly reorder the factor labels so that the control group always ends up in the denominator for the fold change calculation.
* fix for https://github.com/computational-metabolomics/structToolbox/issues/18
fixed incorrect length check on matching class labels.
* Issue 17 ttest factor (#21)
* convert to factor if not one already
fix for issue #17
* update roxygen version
* fix for issue #9 (#22)
changed from lapply to vapply and used drop=FALSE to ensure compatibility with a single factor.
* allow user to set lambda (#24)
- lambda changed to input parameter. NULL = uses pmp optimisation
- model_predict now uses the set value of lambda, or lambda_opt if used.
- documentation updated
* Feature non parametric fold change (#26)
* add "median" method
based on DOI: 10.1080/00949650212140 can now calcuate fold changes equivalent to using medians and corresponding confidence intervals
* update documentation
* update median method
now correctly calculates ratio of medians
* use wilcox for paired median intervals
make use of wilcox.test to estimate intervals for the median when using median for paired samples
* Issue 23 filter by name (#27)
* fix for #23
moved all model_apply functionality to model_predict so that model_train and model_predict can be used as well as model_apply
* update documentation
* Update mean_of_medians.R (#29)
fix for #28
- correctly loop over all levels in the named factor
* Feature documentation 3 12 (#31)
* update documentation
Description and inputs now pulled from the object definitions for consistency.
* fix definition of label_features
allows NULL and description updated
* replace non ascii characters
* export mixed_effect object
* use correct object name to generate documentation
* export mixed_effect object
* remove non ascii characters
* update tests with new object name
* add import for capture.output
* add import for capture.output
* use pca_biplot in tests
chart was renamed
* add utils import
* update struct dependency version
* update documentation
* update news, version bump
Gavin Rhys Lloyd authored on 25/10/2020 08:50:13
• GitHub committed on 25/10/2020 08:50:13
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@@ -2,19 +2,27 @@ |
| 2 | 2 |
% Please edit documentation in R/hca_class.R |
| 3 | 3 |
\name{hca_dendrogram}
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\alias{hca_dendrogram}
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-\title{hca_dendrogram class}
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+\title{HCA dendrogram}
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\usage{
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hca_dendrogram(...) |
| 8 | 8 |
} |
| 9 | 9 |
\arguments{
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-\item{...}{additional slots and values passed to struct_class}
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+\item{...}{Additional slots and values passed to \code{struct_class}.}
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| 11 | 11 |
} |
| 12 | 12 |
\value{
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-struct object |
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+A \code{hca_dendrogram} object.
|
|
| 14 | 14 |
} |
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\description{
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-plots a dendrogram for HCA |
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+A dendrogram visualising the clustering by HCA. |
|
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+} |
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+\details{
|
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+This object makes use of functionality from the following packages:\itemize{\item{\code{ggdendro}}}
|
|
| 17 | 20 |
} |
| 18 | 21 |
\examples{
|
| 19 | 22 |
C = hca_dendrogram() |
| 20 | 23 |
} |
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+\references{
|
|
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+de Vries A, Ripley BD (2020). |
|
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+\emph{ggdendro: Create Dendrograms and Tree Diagrams Using 'ggplot2'}.
|
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+R package version 0.1.22, \url{https://CRAN.R-project.org/package=ggdendro}.
|
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+} |
Gavin Rhys Lloyd authored on 04/02/2020 17:18:11
Gavin Rhys Lloyd authored on 19/12/2019 15:14:02
...update some documentation
Gavin Rhys Lloyd authored on 17/12/2019 17:24:38
...rename all function with dot to underscore
replace dataset with DatasetExperiment
Gavin Rhys Lloyd authored on 17/12/2019 15:48:01
| 1 | 1 |
new file mode 100644 |
| ... | ... |
@@ -0,0 +1,14 @@ |
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+% Generated by roxygen2: do not edit by hand |
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+% Please edit documentation in R/hca_class.R |
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+\name{hca_dendrogram}
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+\alias{hca_dendrogram}
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+\title{hca_dendrogram class}
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+\usage{
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+hca_dendrogram(...) |
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+} |
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+\description{
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+plots a dendrogram for HCA |
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+} |
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+\examples{
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+C = hca_dendrogram() |
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+} |