- due to changes in struct (removal of unicode)
Gavin Rhys Lloyd authored on 02/02/2024 10:50:50
| ... | ... |
@@ -25,7 +25,7 @@ A bar chart of the d-statistics for samples in the input PCA model. Samples abov |
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\section{Inheritance}{
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A \code{pca_dstat_plot} object inherits the following \code{struct} classes: \cr\cr
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-\code{pca_dstat_plot()} ⭢ \code{chart()} ⭢ \code{struct_class()}
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+\verb{[pca_dstat_plot]} >> \verb{[chart]} >> \verb{[struct_class]}
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} |
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\examples{
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- get_description moved to struct and updated
Gavin Rhys Lloyd authored on 31/01/2024 09:48:31
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@@ -7,9 +7,9 @@ |
| 7 | 7 |
pca_dstat_plot(number_components = 2, alpha = 0.05, ...) |
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} |
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\arguments{
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-\item{number_components}{(numeric) The number of principal components to use. The default is \code{2}.}
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+\item{number_components}{(numeric) The number of principal components to use. The default is \code{2}.\cr}
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-\item{alpha}{(numeric) A confidence threshold for rejecting samples based on the d-statistic. The default is \code{0.05}.}
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+\item{alpha}{(numeric) A confidence threshold for rejecting samples based on the d-statistic. The default is \code{0.05}.\cr}
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| 13 | 13 |
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\item{...}{Additional slots and values passed to \code{struct_class}.}
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} |
| ... | ... |
@@ -22,6 +22,16 @@ See \code{\link[struct]{chart_plot}} in the \code{struct} package to plot this c
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\description{
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A bar chart of the d-statistics for samples in the input PCA model. Samples above the indicated threshold are considered to be outlying. |
| 24 | 24 |
} |
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+\section{Inheritance}{
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+ |
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+A \code{pca_dstat_plot} object inherits the following \code{struct} classes: \cr\cr
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+\code{pca_dstat_plot()} ⭢ \code{chart()} ⭢ \code{struct_class()}
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+} |
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+ |
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\examples{
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+M = pca_dstat_plot( |
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+ number_components = 2, |
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+ alpha = 0.95) |
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+ |
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C = pca_dstat_plot() |
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} |
Gavin Rhys Lloyd authored on 07/07/2021 09:37:19
• GitHub committed on 07/07/2021 09:37:19
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@@ -14,7 +14,10 @@ pca_dstat_plot(number_components = 2, alpha = 0.05, ...) |
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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{pca_dstat_plot} object.
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+A \code{
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+pca_dstat_plot |
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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 bar chart of the d-statistics for samples in the input PCA model. Samples above the indicated threshold are considered to be outlying. |
* 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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@@ -2,23 +2,22 @@ |
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% Please edit documentation in R/PCA_plotfcns.R |
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\name{pca_dstat_plot}
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\alias{pca_dstat_plot}
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-\title{pca_dstat_plot_plot class}
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+\title{d-statistic plot}
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\usage{
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pca_dstat_plot(number_components = 2, alpha = 0.05, ...) |
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} |
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\arguments{
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-\item{number_components}{The number of components to use.}
|
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+\item{number_components}{(numeric) The number of principal components to use. The default is \code{2}.}
|
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-\item{alpha}{The confidence level to plot.}
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+\item{alpha}{(numeric) A confidence threshold for rejecting samples based on the d-statistic. The default is \code{0.05}.}
|
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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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} |
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\value{
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-struct object |
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+A \code{pca_dstat_plot} object.
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} |
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\description{
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-Bar chart showing mahalanobis distance from the mean in PCA scores space. A threshold is |
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-plotted at a chosen confidence as an indicator for rejecting outliers. |
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+A bar chart of the d-statistics for samples in the input PCA model. Samples above the indicated threshold are considered to be outlying. |
|
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} |
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\examples{
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C = pca_dstat_plot() |
Gavin Rhys Lloyd authored on 11/02/2020 13:19:28
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new file mode 100644 |
| ... | ... |
@@ -0,0 +1,25 @@ |
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+% Generated by roxygen2: do not edit by hand |
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+% Please edit documentation in R/PCA_plotfcns.R |
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+\name{pca_dstat_plot}
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+\alias{pca_dstat_plot}
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+\title{pca_dstat_plot_plot class}
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+\usage{
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+pca_dstat_plot(number_components = 2, alpha = 0.05, ...) |
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+} |
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+\arguments{
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+\item{number_components}{The number of components to use.}
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+ |
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+\item{alpha}{The confidence level to plot.}
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+ |
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+\item{...}{additional slots and values passed to struct_class}
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+} |
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+\value{
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+struct object |
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+} |
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+\description{
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+Bar chart showing mahalanobis distance from the mean in PCA scores space. A threshold is |
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+plotted at a chosen confidence as an indicator for rejecting outliers. |
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+} |
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+\examples{
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+C = pca_dstat_plot() |
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+} |