- due to changes in struct (removal of unicode)
Gavin Rhys Lloyd authored on 02/02/2024 10:50:50
| ... | ... |
@@ -28,7 +28,7 @@ This object makes use of functionality from the following packages:\itemize{ \i
|
| 28 | 28 |
\section{Inheritance}{
|
| 29 | 29 |
|
| 30 | 30 |
A \code{plsda_roc_plot} object inherits the following \code{struct} classes: \cr\cr
|
| 31 |
-\code{plsda_roc_plot()} ⭢ \code{chart()} ⭢ \code{struct_class()}
|
|
| 31 |
+\verb{[plsda_roc_plot]} >> \verb{[chart]} >> \verb{[struct_class]}
|
|
| 32 | 32 |
} |
| 33 | 33 |
|
| 34 | 34 |
\examples{
|
- get_description moved to struct and updated
Gavin Rhys Lloyd authored on 31/01/2024 09:48:31
| ... | ... |
@@ -9,7 +9,7 @@ plsda_roc_plot(factor_name, ycol = 1, ...) |
| 9 | 9 |
\arguments{
|
| 10 | 10 |
\item{factor_name}{(character) The name of a sample-meta column to use.}
|
| 11 | 11 |
|
| 12 |
-\item{ycol}{(character, numeric, integer) The column of the Y block to be plotted. The default is \code{1}.}
|
|
| 12 |
+\item{ycol}{(character, numeric, integer) The column of the Y block to be plotted. The default is \code{1}.\cr}
|
|
| 13 | 13 |
|
| 14 | 14 |
\item{...}{Additional slots and values passed to \code{struct_class}.}
|
| 15 | 15 |
} |
| ... | ... |
@@ -23,9 +23,19 @@ See \code{\link[struct]{chart_plot}} in the \code{struct} package to plot this c
|
| 23 | 23 |
A Receiver Operator Characteristic (ROC) plot for PLSDA models computed by adjusting the threshold for assigning group labels from PLS predictions. |
| 24 | 24 |
} |
| 25 | 25 |
\details{
|
| 26 |
-This object makes use of functionality from the following packages:\itemize{\item{\code{pls}}\item{\code{ggplot2}}}
|
|
| 26 |
+This object makes use of functionality from the following packages:\itemize{ \item{\code{pls}} \item{\code{ggplot2}}}
|
|
| 27 | 27 |
} |
| 28 |
+\section{Inheritance}{
|
|
| 29 |
+ |
|
| 30 |
+A \code{plsda_roc_plot} object inherits the following \code{struct} classes: \cr\cr
|
|
| 31 |
+\code{plsda_roc_plot()} ⭢ \code{chart()} ⭢ \code{struct_class()}
|
|
| 32 |
+} |
|
| 33 |
+ |
|
| 28 | 34 |
\examples{
|
| 35 |
+M = plsda_roc_plot( |
|
| 36 |
+ factor_name = "V1", |
|
| 37 |
+ ycol = 1) |
|
| 38 |
+ |
|
| 29 | 39 |
D = iris_DatasetExperiment() |
| 30 | 40 |
M = mean_centre()+PLSDA(factor_name='Species') |
| 31 | 41 |
M = model_apply(M,D) |
| ... | ... |
@@ -35,7 +45,7 @@ chart_plot(C,M[2]) |
| 35 | 45 |
} |
| 36 | 46 |
\references{
|
| 37 | 47 |
Liland K, Mevik B, Wehrens R (2023). \emph{pls: Partial Least Squares and
|
| 38 |
-Principal Component Regression}. R package version 2.8-2, |
|
| 48 |
+Principal Component Regression}. R package version 2.8-3, |
|
| 39 | 49 |
\url{https://CRAN.R-project.org/package=pls}.
|
| 40 | 50 |
|
| 41 | 51 |
Wickham H (2016). \emph{ggplot2: Elegant Graphics for Data Analysis}.
|
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
| ... | ... |
@@ -34,12 +34,11 @@ C = plsda_roc_plot(factor_name='Species') |
| 34 | 34 |
chart_plot(C,M[2]) |
| 35 | 35 |
} |
| 36 | 36 |
\references{
|
| 37 |
-Liland K, Mevik B, Wehrens R (2022). |
|
| 38 |
-\emph{pls: Partial Least Squares and Principal Component Regression}.
|
|
| 39 |
-R package version 2.8-1, \url{https://CRAN.R-project.org/package=pls}.
|
|
| 37 |
+Liland K, Mevik B, Wehrens R (2023). \emph{pls: Partial Least Squares and
|
|
| 38 |
+Principal Component Regression}. R package version 2.8-2, |
|
| 39 |
+\url{https://CRAN.R-project.org/package=pls}.
|
|
| 40 | 40 |
|
| 41 |
-Wickham H (2016). |
|
| 42 |
-\emph{ggplot2: Elegant Graphics for Data Analysis}.
|
|
| 43 |
-Springer-Verlag New York. |
|
| 44 |
-ISBN 978-3-319-24277-4, \url{https://ggplot2.tidyverse.org}.
|
|
| 41 |
+Wickham H (2016). \emph{ggplot2: Elegant Graphics for Data Analysis}.
|
|
| 42 |
+Springer-Verlag New York. ISBN 978-3-319-24277-4, |
|
| 43 |
+\url{https://ggplot2.tidyverse.org}.
|
|
| 45 | 44 |
} |
Gavin Rhys Lloyd authored on 23/01/2023 10:57:52
| ... | ... |
@@ -34,9 +34,9 @@ C = plsda_roc_plot(factor_name='Species') |
| 34 | 34 |
chart_plot(C,M[2]) |
| 35 | 35 |
} |
| 36 | 36 |
\references{
|
| 37 |
-Liland K, Mevik B, Wehrens R (2021). |
|
| 37 |
+Liland K, Mevik B, Wehrens R (2022). |
|
| 38 | 38 |
\emph{pls: Partial Least Squares and Principal Component Regression}.
|
| 39 |
-R package version 2.8-0, \url{https://CRAN.R-project.org/package=pls}.
|
|
| 39 |
+R package version 2.8-1, \url{https://CRAN.R-project.org/package=pls}.
|
|
| 40 | 40 |
|
| 41 | 41 |
Wickham H (2016). |
| 42 | 42 |
\emph{ggplot2: Elegant Graphics for Data Analysis}.
|
* add selectivity ratio
* replace vip_summary with feature_importance
renamed and now allows vip, sr and sr_pvalues to be plotted
* add equal_split model
random subsets so generate training sets with equal group numbers
* plot 1 - p-value
to conform with the "best" feature being a maximum value
* add resample iterator
subsample at random over a number of iterations. Option to use
different kinds of splitting methods. Corresponding chart.
* allow use of list() for factor_name
* force apply not to simplify output to guarantee returning a list
* update example
* add correct parameter
collect will collect the requested model output over all iterations in a list WORK IN PROGRESS
* add collection of multiple outputs of model sequence
* plot reg coeff on rhs
* match outputs of xval for use with grid search etc
* specify levels when converting predictions to factor
* change PLSDA to inherit from PLSR
rename some charts to be compatible with both PLSR and PLSDA
* allow y-block column selection
* re-assign y output after PLSR with factor
* update vignettes wrt PLS changes
* update documentation
* update R version to 4.1
* update documentation
* update documentation
* update scatter plot
- new scatter chart object
- used by PCA scores, PLSR/PLSDA scores
- other charts updated to reflect changes in scores plots where necessary
- added ycol param to plots for when y-block is a matrix
* add url to github
* add plsda scores alias
- plsda_scores_plot and pls_scores_plot do that same thing
Included for backwards compatability
- added components back as parameter for scores plots for backwards compatibility
* fix broken example
* fix broken tests
- scores is now returned as a DatasetExperiment object not a data.frame
* Update data_analysis_omics_using_the_structtoolbox.Rmd
- wrt changes in scores plots
* update documentation
* fix colnames for Y matrix
Gavin Rhys Lloyd authored on 28/02/2022 12:38:08
• GitHub committed on 28/02/2022 12:38:08
| ... | ... |
@@ -4,11 +4,13 @@ |
| 4 | 4 |
\alias{plsda_roc_plot}
|
| 5 | 5 |
\title{PLSDA ROC plot}
|
| 6 | 6 |
\usage{
|
| 7 |
-plsda_roc_plot(factor_name, ...) |
|
| 7 |
+plsda_roc_plot(factor_name, ycol = 1, ...) |
|
| 8 | 8 |
} |
| 9 | 9 |
\arguments{
|
| 10 | 10 |
\item{factor_name}{(character) The name of a sample-meta column to use.}
|
| 11 | 11 |
|
| 12 |
+\item{ycol}{(character, numeric, integer) The column of the Y block to be plotted. The default is \code{1}.}
|
|
| 13 |
+ |
|
| 12 | 14 |
\item{...}{Additional slots and values passed to \code{struct_class}.}
|
| 13 | 15 |
} |
| 14 | 16 |
\value{
|
Gavin Rhys Lloyd authored on 01/10/2021 16:52:55
| ... | ... |
@@ -32,9 +32,9 @@ C = plsda_roc_plot(factor_name='Species') |
| 32 | 32 |
chart_plot(C,M[2]) |
| 33 | 33 |
} |
| 34 | 34 |
\references{
|
| 35 |
-Mevik B, Wehrens R, Liland K (2020). |
|
| 35 |
+Liland K, Mevik B, Wehrens R (2021). |
|
| 36 | 36 |
\emph{pls: Partial Least Squares and Principal Component Regression}.
|
| 37 |
-R package version 2.7-3, \url{https://CRAN.R-project.org/package=pls}.
|
|
| 37 |
+R package version 2.8-0, \url{https://CRAN.R-project.org/package=pls}.
|
|
| 38 | 38 |
|
| 39 | 39 |
Wickham H (2016). |
| 40 | 40 |
\emph{ggplot2: Elegant Graphics for Data Analysis}.
|
Gavin Rhys Lloyd authored on 07/07/2021 09:37:19
• GitHub committed on 07/07/2021 09:37:19
| ... | ... |
@@ -12,7 +12,10 @@ plsda_roc_plot(factor_name, ...) |
| 12 | 12 |
\item{...}{Additional slots and values passed to \code{struct_class}.}
|
| 13 | 13 |
} |
| 14 | 14 |
\value{
|
| 15 |
-A \code{plsda_roc_plot} object.
|
|
| 15 |
+A \code{
|
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| 16 |
+plsda_roc_plot |
|
| 17 |
+} object. This object has no \code{output} slots.
|
|
| 18 |
+See \code{\link[struct]{chart_plot}} in the \code{struct} package to plot this chart object.
|
|
| 16 | 19 |
} |
| 17 | 20 |
\description{
|
| 18 | 21 |
A Receiver Operator Characteristic (ROC) plot for PLSDA models computed by adjusting the threshold for assigning group labels from PLS predictions. |
* 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
| ... | ... |
@@ -2,20 +2,23 @@ |
| 2 | 2 |
% Please edit documentation in R/PLSDA_charts.R |
| 3 | 3 |
\name{plsda_roc_plot}
|
| 4 | 4 |
\alias{plsda_roc_plot}
|
| 5 |
-\title{plsda_roc_plot class}
|
|
| 5 |
+\title{PLSDA ROC plot}
|
|
| 6 | 6 |
\usage{
|
| 7 | 7 |
plsda_roc_plot(factor_name, ...) |
| 8 | 8 |
} |
| 9 | 9 |
\arguments{
|
| 10 |
-\item{factor_name}{The sample_meta column name to use}
|
|
| 10 |
+\item{factor_name}{(character) The name of a sample-meta column to use.}
|
|
| 11 | 11 |
|
| 12 |
-\item{...}{additional slots and values passed to struct_class}
|
|
| 12 |
+\item{...}{Additional slots and values passed to \code{struct_class}.}
|
|
| 13 | 13 |
} |
| 14 | 14 |
\value{
|
| 15 |
-struct object |
|
| 15 |
+A \code{plsda_roc_plot} object.
|
|
| 16 | 16 |
} |
| 17 | 17 |
\description{
|
| 18 |
-Plots the ROC curve of a PLSDA model. Only suitable for two classes. |
|
| 18 |
+A Receiver Operator Characteristic (ROC) plot for PLSDA models computed by adjusting the threshold for assigning group labels from PLS predictions. |
|
| 19 |
+} |
|
| 20 |
+\details{
|
|
| 21 |
+This object makes use of functionality from the following packages:\itemize{\item{\code{pls}}\item{\code{ggplot2}}}
|
|
| 19 | 22 |
} |
| 20 | 23 |
\examples{
|
| 21 | 24 |
D = iris_DatasetExperiment() |
| ... | ... |
@@ -25,3 +28,13 @@ M = model_apply(M,D) |
| 25 | 28 |
C = plsda_roc_plot(factor_name='Species') |
| 26 | 29 |
chart_plot(C,M[2]) |
| 27 | 30 |
} |
| 31 |
+\references{
|
|
| 32 |
+Mevik B, Wehrens R, Liland K (2020). |
|
| 33 |
+\emph{pls: Partial Least Squares and Principal Component Regression}.
|
|
| 34 |
+R package version 2.7-3, \url{https://CRAN.R-project.org/package=pls}.
|
|
| 35 |
+ |
|
| 36 |
+Wickham H (2016). |
|
| 37 |
+\emph{ggplot2: Elegant Graphics for Data Analysis}.
|
|
| 38 |
+Springer-Verlag New York. |
|
| 39 |
+ISBN 978-3-319-24277-4, \url{https://ggplot2.tidyverse.org}.
|
|
| 40 |
+} |
+ AUC metric
+ PLS charts (reg coeff, ROC, VIP scores)
+ stratified data set splitting
Gavin Rhys Lloyd authored on 07/04/2020 14:39:32
| 1 | 1 |
new file mode 100644 |
| ... | ... |
@@ -0,0 +1,27 @@ |
| 1 |
+% Generated by roxygen2: do not edit by hand |
|
| 2 |
+% Please edit documentation in R/PLSDA_charts.R |
|
| 3 |
+\name{plsda_roc_plot}
|
|
| 4 |
+\alias{plsda_roc_plot}
|
|
| 5 |
+\title{plsda_roc_plot class}
|
|
| 6 |
+\usage{
|
|
| 7 |
+plsda_roc_plot(factor_name, ...) |
|
| 8 |
+} |
|
| 9 |
+\arguments{
|
|
| 10 |
+\item{factor_name}{The sample_meta column name to use}
|
|
| 11 |
+ |
|
| 12 |
+\item{...}{additional slots and values passed to struct_class}
|
|
| 13 |
+} |
|
| 14 |
+\value{
|
|
| 15 |
+struct object |
|
| 16 |
+} |
|
| 17 |
+\description{
|
|
| 18 |
+Plots the ROC curve of a PLSDA model. Only suitable for two classes. |
|
| 19 |
+} |
|
| 20 |
+\examples{
|
|
| 21 |
+D = iris_DatasetExperiment() |
|
| 22 |
+M = mean_centre()+PLSDA(factor_name='Species') |
|
| 23 |
+M = model_apply(M,D) |
|
| 24 |
+ |
|
| 25 |
+C = plsda_roc_plot(factor_name='Species') |
|
| 26 |
+chart_plot(C,M[2]) |
|
| 27 |
+} |