- due to changes in struct (removal of unicode)
Gavin Rhys Lloyd authored on 02/02/2024 10:50:50
| ... | ... |
@@ -37,7 +37,7 @@ A boxplot to visualise the distribution of values within a subset of features. |
| 37 | 37 |
\section{Inheritance}{
|
| 38 | 38 |
|
| 39 | 39 |
A \code{DatasetExperiment_boxplot} object inherits the following \code{struct} classes: \cr\cr
|
| 40 |
-\code{DatasetExperiment_boxplot()} ⭢ \code{chart()} ⭢ \code{struct_class()}
|
|
| 40 |
+\verb{[DatasetExperiment_boxplot]} >> \verb{[chart]} >> \verb{[struct_class]}
|
|
| 41 | 41 |
} |
| 42 | 42 |
|
| 43 | 43 |
\examples{
|
- get_description moved to struct and updated
Gavin Rhys Lloyd authored on 31/01/2024 09:48:31
| ... | ... |
@@ -15,11 +15,11 @@ DatasetExperiment_boxplot( |
| 15 | 15 |
\arguments{
|
| 16 | 16 |
\item{factor_name}{(character) The name of a sample-meta column to use.}
|
| 17 | 17 |
|
| 18 |
-\item{by_sample}{(logical) Plot by sample. Allowed values are limited to the following: \itemize{\item{\code{"TRUE"}: The data is plotted across features for a subset of samples.}\item{\code{"FALSE"}: The data is plotted across samples for a subset of features.}} The default is \code{TRUE}.}
|
|
| 18 |
+\item{by_sample}{(logical) Plot by sample. Allowed values are limited to the following: \itemize{ \item{\code{"TRUE"}: The data is plotted across features for a subset of samples.}\item{\code{"FALSE"}: The data is plotted across samples for a subset of features.}} The default is \code{TRUE}.\cr}
|
|
| 19 | 19 |
|
| 20 |
-\item{per_class}{(logical) Plot per class. Allowed values are limited to the following: \itemize{\item{\code{"TRUE"}: The data is plotted for each class.}\item{\code{"FALSE"}: The data is plotted for all samples.}} The default is \code{TRUE}.}
|
|
| 20 |
+\item{per_class}{(logical) Plot per class. Allowed values are limited to the following: \itemize{ \item{\code{"TRUE"}: The data is plotted for each class.}\item{\code{"FALSE"}: The data is plotted for all samples.}} The default is \code{TRUE}.\cr}
|
|
| 21 | 21 |
|
| 22 |
-\item{number}{(numeric, integer) The number of features/samples plotted. The default is \code{50}.}
|
|
| 22 |
+\item{number}{(numeric, integer) The number of features/samples plotted. The default is \code{50}.\cr}
|
|
| 23 | 23 |
|
| 24 | 24 |
\item{...}{Additional slots and values passed to \code{struct_class}.}
|
| 25 | 25 |
} |
| ... | ... |
@@ -34,7 +34,19 @@ struct object |
| 34 | 34 |
\description{
|
| 35 | 35 |
A boxplot to visualise the distribution of values within a subset of features. |
| 36 | 36 |
} |
| 37 |
+\section{Inheritance}{
|
|
| 38 |
+ |
|
| 39 |
+A \code{DatasetExperiment_boxplot} object inherits the following \code{struct} classes: \cr\cr
|
|
| 40 |
+\code{DatasetExperiment_boxplot()} ⭢ \code{chart()} ⭢ \code{struct_class()}
|
|
| 41 |
+} |
|
| 42 |
+ |
|
| 37 | 43 |
\examples{
|
| 44 |
+M = DatasetExperiment_boxplot( |
|
| 45 |
+ factor_name = "V1", |
|
| 46 |
+ by_sample = FALSE, |
|
| 47 |
+ per_class = FALSE, |
|
| 48 |
+ number = 50) |
|
| 49 |
+ |
|
| 38 | 50 |
D = MTBLS79_DatasetExperiment() |
| 39 | 51 |
C = DatasetExperiment_boxplot(factor_name='Class',number=10,per_class=FALSE) |
| 40 | 52 |
chart_plot(C,D) |
Gavin Rhys Lloyd authored on 07/07/2021 09:37:19
• GitHub committed on 07/07/2021 09:37:19
| ... | ... |
@@ -24,7 +24,10 @@ DatasetExperiment_boxplot( |
| 24 | 24 |
\item{...}{Additional slots and values passed to \code{struct_class}.}
|
| 25 | 25 |
} |
| 26 | 26 |
\value{
|
| 27 |
-A \code{DatasetExperiment_boxplot} object.
|
|
| 27 |
+A \code{
|
|
| 28 |
+DatasetExperiment_boxplot |
|
| 29 |
+} object. This object has no \code{output} slots.
|
|
| 30 |
+See \code{\link[struct]{chart_plot}} in the \code{struct} package to plot this chart object.
|
|
| 28 | 31 |
|
| 29 | 32 |
struct object |
| 30 | 33 |
} |
occurred due to capitalisation of some column names in sample meta of MTBLS79 in pmp
Gavin Rhys Lloyd authored on 26/04/2021 15:00:13
| ... | ... |
@@ -33,6 +33,6 @@ A boxplot to visualise the distribution of values within a subset of features. |
| 33 | 33 |
} |
| 34 | 34 |
\examples{
|
| 35 | 35 |
D = MTBLS79_DatasetExperiment() |
| 36 |
-C = DatasetExperiment_boxplot(factor_name='class',number=10,per_class=FALSE) |
|
| 36 |
+C = DatasetExperiment_boxplot(factor_name='Class',number=10,per_class=FALSE) |
|
| 37 | 37 |
chart_plot(C,D) |
| 38 | 38 |
} |
* 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
| ... | ... |
@@ -2,7 +2,7 @@ |
| 2 | 2 |
% Please edit documentation in R/dataset_chart_classes.R |
| 3 | 3 |
\name{DatasetExperiment_boxplot}
|
| 4 | 4 |
\alias{DatasetExperiment_boxplot}
|
| 5 |
-\title{DatasetExperiment boxplot}
|
|
| 5 |
+\title{Feature distribution histogram}
|
|
| 6 | 6 |
\usage{
|
| 7 | 7 |
DatasetExperiment_boxplot( |
| 8 | 8 |
factor_name, |
| ... | ... |
@@ -13,25 +13,26 @@ DatasetExperiment_boxplot( |
| 13 | 13 |
) |
| 14 | 14 |
} |
| 15 | 15 |
\arguments{
|
| 16 |
-\item{factor_name}{the column name of sample_meta to use}
|
|
| 16 |
+\item{factor_name}{(character) The name of a sample-meta column to use.}
|
|
| 17 | 17 |
|
| 18 |
-\item{by_sample}{[TRUE] or FALSE to plot by samples or features respectively}
|
|
| 18 |
+\item{by_sample}{(logical) Plot by sample. Allowed values are limited to the following: \itemize{\item{\code{"TRUE"}: The data is plotted across features for a subset of samples.}\item{\code{"FALSE"}: The data is plotted across samples for a subset of features.}} The default is \code{TRUE}.}
|
|
| 19 | 19 |
|
| 20 |
-\item{per_class}{[TRUE] or FALSE to plot per level in factro_name}
|
|
| 20 |
+\item{per_class}{(logical) Plot per class. Allowed values are limited to the following: \itemize{\item{\code{"TRUE"}: The data is plotted for each class.}\item{\code{"FALSE"}: The data is plotted for all samples.}} The default is \code{TRUE}.}
|
|
| 21 | 21 |
|
| 22 |
-\item{number}{the number of samples/features to plot}
|
|
| 22 |
+\item{number}{(numeric, integer) The number of features/samples plotted. The default is \code{50}.}
|
|
| 23 | 23 |
|
| 24 |
-\item{...}{additional slots and values passed to struct_class}
|
|
| 24 |
+\item{...}{Additional slots and values passed to \code{struct_class}.}
|
|
| 25 | 25 |
} |
| 26 | 26 |
\value{
|
| 27 |
+A \code{DatasetExperiment_boxplot} object.
|
|
| 28 |
+ |
|
| 27 | 29 |
struct object |
| 28 | 30 |
} |
| 29 | 31 |
\description{
|
| 30 |
-Boxplot of values per sample/feature in a DatasetExperiment |
|
| 32 |
+A boxplot to visualise the distribution of values within a subset of features. |
|
| 31 | 33 |
} |
| 32 | 34 |
\examples{
|
| 33 | 35 |
D = MTBLS79_DatasetExperiment() |
| 34 | 36 |
C = DatasetExperiment_boxplot(factor_name='class',number=10,per_class=FALSE) |
| 35 | 37 |
chart_plot(C,D) |
| 36 |
- |
|
| 37 | 38 |
} |
Gavin Rhys Lloyd authored on 11/02/2020 13:19:28
| 1 | 1 |
new file mode 100644 |
| ... | ... |
@@ -0,0 +1,37 @@ |
| 1 |
+% Generated by roxygen2: do not edit by hand |
|
| 2 |
+% Please edit documentation in R/dataset_chart_classes.R |
|
| 3 |
+\name{DatasetExperiment_boxplot}
|
|
| 4 |
+\alias{DatasetExperiment_boxplot}
|
|
| 5 |
+\title{DatasetExperiment boxplot}
|
|
| 6 |
+\usage{
|
|
| 7 |
+DatasetExperiment_boxplot( |
|
| 8 |
+ factor_name, |
|
| 9 |
+ by_sample = TRUE, |
|
| 10 |
+ per_class = TRUE, |
|
| 11 |
+ number = 50, |
|
| 12 |
+ ... |
|
| 13 |
+) |
|
| 14 |
+} |
|
| 15 |
+\arguments{
|
|
| 16 |
+\item{factor_name}{the column name of sample_meta to use}
|
|
| 17 |
+ |
|
| 18 |
+\item{by_sample}{[TRUE] or FALSE to plot by samples or features respectively}
|
|
| 19 |
+ |
|
| 20 |
+\item{per_class}{[TRUE] or FALSE to plot per level in factro_name}
|
|
| 21 |
+ |
|
| 22 |
+\item{number}{the number of samples/features to plot}
|
|
| 23 |
+ |
|
| 24 |
+\item{...}{additional slots and values passed to struct_class}
|
|
| 25 |
+} |
|
| 26 |
+\value{
|
|
| 27 |
+struct object |
|
| 28 |
+} |
|
| 29 |
+\description{
|
|
| 30 |
+Boxplot of values per sample/feature in a DatasetExperiment |
|
| 31 |
+} |
|
| 32 |
+\examples{
|
|
| 33 |
+D = MTBLS79_DatasetExperiment() |
|
| 34 |
+C = DatasetExperiment_boxplot(factor_name='class',number=10,per_class=FALSE) |
|
| 35 |
+chart_plot(C,D) |
|
| 36 |
+ |
|
| 37 |
+} |