- due to changes in struct (removal of unicode)
Gavin Rhys Lloyd authored on 02/02/2024 10:50:50
| ... | ... |
@@ -23,7 +23,7 @@ Histograms and boxplots computed across samples and features are used to visuall |
| 23 | 23 |
\section{Inheritance}{
|
| 24 | 24 |
|
| 25 | 25 |
A \code{compare_dist} object inherits the following \code{struct} classes: \cr\cr
|
| 26 |
-\code{compare_dist()} ⭢ \code{chart()} ⭢ \code{struct_class()}
|
|
| 26 |
+\verb{[compare_dist]} >> \verb{[chart]} >> \verb{[struct_class]}
|
|
| 27 | 27 |
} |
| 28 | 28 |
|
| 29 | 29 |
\examples{
|
- get_description moved to struct and updated
Gavin Rhys Lloyd authored on 31/01/2024 09:48:31
| ... | ... |
@@ -20,7 +20,16 @@ See \code{\link[struct]{chart_plot}} in the \code{struct} package to plot this c
|
| 20 | 20 |
\description{
|
| 21 | 21 |
Histograms and boxplots computed across samples and features are used to visually compare two datasets e.g. before and after filtering and/or normalisation. |
| 22 | 22 |
} |
| 23 |
+\section{Inheritance}{
|
|
| 24 |
+ |
|
| 25 |
+A \code{compare_dist} object inherits the following \code{struct} classes: \cr\cr
|
|
| 26 |
+\code{compare_dist()} ⭢ \code{chart()} ⭢ \code{struct_class()}
|
|
| 27 |
+} |
|
| 28 |
+ |
|
| 23 | 29 |
\examples{
|
| 30 |
+M = compare_dist( |
|
| 31 |
+ factor_name = "V1") |
|
| 32 |
+ |
|
| 24 | 33 |
D1=MTBLS79_DatasetExperiment(filtered=FALSE) |
| 25 | 34 |
D2=MTBLS79_DatasetExperiment(filtered=TRUE) |
| 26 | 35 |
C = compare_dist(factor_name='Class') |
Gavin Rhys Lloyd authored on 07/07/2021 09:37:19
• GitHub committed on 07/07/2021 09:37:19
| ... | ... |
@@ -12,7 +12,10 @@ compare_dist(factor_name, ...) |
| 12 | 12 |
\item{...}{Additional slots and values passed to \code{struct_class}.}
|
| 13 | 13 |
} |
| 14 | 14 |
\value{
|
| 15 |
-A \code{compare_dist} object.
|
|
| 15 |
+A \code{
|
|
| 16 |
+compare_dist |
|
| 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 |
Histograms and boxplots computed across samples and features are used to visually compare two datasets e.g. before and after filtering and/or normalisation. |
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
| ... | ... |
@@ -20,6 +20,6 @@ Histograms and boxplots computed across samples and features are used to visuall |
| 20 | 20 |
\examples{
|
| 21 | 21 |
D1=MTBLS79_DatasetExperiment(filtered=FALSE) |
| 22 | 22 |
D2=MTBLS79_DatasetExperiment(filtered=TRUE) |
| 23 |
-C = compare_dist(factor_name='class') |
|
| 23 |
+C = compare_dist(factor_name='Class') |
|
| 24 | 24 |
chart_plot(C,D1,D2) |
| 25 | 25 |
} |
* 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
| ... | ... |
@@ -7,16 +7,15 @@ |
| 7 | 7 |
compare_dist(factor_name, ...) |
| 8 | 8 |
} |
| 9 | 9 |
\arguments{
|
| 10 |
-\item{factor_name}{the sample_meta colum 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{compare_dist} object.
|
|
| 16 | 16 |
} |
| 17 | 17 |
\description{
|
| 18 |
-A combination of plots to compare distributions of samples/features in two |
|
| 19 |
-datasets |
|
| 18 |
+Histograms and boxplots computed across samples and features are used to visually compare two datasets e.g. before and after filtering and/or normalisation. |
|
| 20 | 19 |
} |
| 21 | 20 |
\examples{
|
| 22 | 21 |
D1=MTBLS79_DatasetExperiment(filtered=FALSE) |
Gavin Rhys Lloyd authored on 11/02/2020 13:19:28
| ... | ... |
@@ -19,8 +19,8 @@ A combination of plots to compare distributions of samples/features in two |
| 19 | 19 |
datasets |
| 20 | 20 |
} |
| 21 | 21 |
\examples{
|
| 22 |
-D1=sbcms_DatasetExperiment(filtered=FALSE) |
|
| 23 |
-D2=sbcms_DatasetExperiment(filtered=TRUE) |
|
| 22 |
+D1=MTBLS79_DatasetExperiment(filtered=FALSE) |
|
| 23 |
+D2=MTBLS79_DatasetExperiment(filtered=TRUE) |
|
| 24 | 24 |
C = compare_dist(factor_name='class') |
| 25 | 25 |
chart_plot(C,D1,D2) |
| 26 | 26 |
} |
Gavin Rhys Lloyd authored on 04/02/2020 17:18:11
| ... | ... |
@@ -4,10 +4,12 @@ |
| 4 | 4 |
\alias{compare_dist}
|
| 5 | 5 |
\title{Compare distributions}
|
| 6 | 6 |
\usage{
|
| 7 |
-compare_dist(...) |
|
| 7 |
+compare_dist(factor_name, ...) |
|
| 8 | 8 |
} |
| 9 | 9 |
\arguments{
|
| 10 |
-\item{...}{slots and values for the new object}
|
|
| 10 |
+\item{factor_name}{the sample_meta colum to use}
|
|
| 11 |
+ |
|
| 12 |
+\item{...}{additional slots and values passed to struct_class}
|
|
| 11 | 13 |
} |
| 12 | 14 |
\value{
|
| 13 | 15 |
struct object |
| ... | ... |
@@ -16,12 +18,6 @@ struct object |
| 16 | 18 |
A combination of plots to compare distributions of samples/features in two |
| 17 | 19 |
datasets |
| 18 | 20 |
} |
| 19 |
-\section{Slots}{
|
|
| 20 |
- |
|
| 21 |
-\describe{
|
|
| 22 |
-\item{\code{factor_name}}{the sample_meta colum to use}
|
|
| 23 |
-}} |
|
| 24 |
- |
|
| 25 | 21 |
\examples{
|
| 26 | 22 |
D1=sbcms_DatasetExperiment(filtered=FALSE) |
| 27 | 23 |
D2=sbcms_DatasetExperiment(filtered=TRUE) |
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
| ... | ... |
@@ -7,12 +7,18 @@ |
| 7 | 7 |
compare_dist(...) |
| 8 | 8 |
} |
| 9 | 9 |
\arguments{
|
| 10 |
-\item{factor_name}{the sample_meta colum to use}
|
|
| 10 |
+\item{...}{slots and values for the new object}
|
|
| 11 | 11 |
} |
| 12 | 12 |
\description{
|
| 13 | 13 |
A combination of plots to compare distributions of samples/features in two |
| 14 | 14 |
datasets |
| 15 | 15 |
} |
| 16 |
+\section{Slots}{
|
|
| 17 |
+ |
|
| 18 |
+\describe{
|
|
| 19 |
+\item{\code{factor_name}}{the sample_meta colum to use}
|
|
| 20 |
+}} |
|
| 21 |
+ |
|
| 16 | 22 |
\examples{
|
| 17 | 23 |
D1=sbcms_DatasetExperiment(filtered=FALSE) |
| 18 | 24 |
D2=sbcms_DatasetExperiment(filtered=TRUE) |
...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 +1,21 @@ |
| 1 |
+% Generated by roxygen2: do not edit by hand |
|
| 2 |
+% Please edit documentation in R/dataset_chart_classes.R |
|
| 3 |
+\name{compare_dist}
|
|
| 4 |
+\alias{compare_dist}
|
|
| 5 |
+\title{Compare distributions}
|
|
| 6 |
+\usage{
|
|
| 7 |
+compare_dist(...) |
|
| 8 |
+} |
|
| 9 |
+\arguments{
|
|
| 10 |
+\item{factor_name}{the sample_meta colum to use}
|
|
| 11 |
+} |
|
| 12 |
+\description{
|
|
| 13 |
+A combination of plots to compare distributions of samples/features in two |
|
| 14 |
+datasets |
|
| 15 |
+} |
|
| 16 |
+\examples{
|
|
| 17 |
+D1=sbcms_DatasetExperiment(filtered=FALSE) |
|
| 18 |
+D2=sbcms_DatasetExperiment(filtered=TRUE) |
|
| 19 |
+C = compare_dist(factor_name='class') |
|
| 20 |
+chart_plot(C,D1,D2) |
|
| 21 |
+} |