plotDensOneAnnotInAllComp
(Package: MineICA) :
Tests if groups of samples are differently distributed on the components and do the corresponding plots.
Given a variable of the phenotype data (i.e vector of sample annotations), this function tests if the groups of samples formed by this variable are differently distributed on the components, in terms of contribution values. The distribution of the groups on the components are represented using density plots. It is possible to restrict the tests and the plots to a subset of samples and/or components.
● Data Source:
BioConductor
● Keywords: internal
● Alias: plotDensOneAnnotInAllComp
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plotMclust
(Package: MineICA) :
Plots the Gaussian fitted by code{link[mclust]{Mclust
Given a result of function Mclust applied on a numeric vector, this function add the fitted Gaussian to a previous plot. This is an internal function called by plotPosSamplesInComp.
● Data Source:
BioConductor
● Keywords: internal
● Alias: plotMclust
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1 images
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plotMix
(Package: MineICA) :
Plots an histogram and Gaussian fitted by code{link[mclust]{Mclust
Given a result of function Mclust applied to a numeric vector, this function draws the fitted Gaussian on the histogram of the data values.
● Data Source:
BioConductor
● Keywords:
● Alias: plotMix
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1 images
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plotPosAnnotInComp
(Package: MineICA) :
Histograms of sample contributions for each annotation level
This function plots the positions of groups of samples formed by the variables (i.e the sample annotations) across all the components of an object of class icaSet. For each variable level (e.g for each tumor stage) this function plots the positions of the corresponding samples (e.g the subset of samples having this tumor stage) within the histogram of the global sample contributions. The plots are saved in pdf file, one file is created per variable. The pdf files are names 'variable.pdf' and save either in pathPlot if specified or the current directory.
● Data Source:
BioConductor
● Keywords:
● Alias: plotPosAnnotInComp
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plotPosOneAnnotInComp_ggplot
(Package: MineICA) :
Tests if groups of samples are differently distributed on the components and do the corresponding plots.
Given a variable of the phenoData, this function tests if the groups of samples formed by this variable are differently distributed, in terms of contribution value (i.e of values in matrix A(icaSet)), on the components. The distribution of the groups on the components are represented using density plots. It is possible to restrict the tests and the plots to a subset of samples and/or components.
● Data Source:
BioConductor
● Keywords: internal
● Alias: plotPosOneAnnotInComp_ggplot
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plotPosOneAnnotLevInComp_ggplot
(Package: MineICA) :
Plots the position of a subset of samples in the histogram of all samples using code{link{ggplot2
Given a sample annotation (e.g a tumor specific stage), this function plots the positions of the corresponding samples (e.g the subset of samples having this tumor stage) within the histogram of the global sample contributions. This function is called by plotPosOneAnnotInComp_ggplot and is only dedicated to the plot of the histogram using the package ggplot2.
● Data Source:
BioConductor
● Keywords: internal
● Alias: plotPosOneAnnotLevInComp_ggplot
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This function plots the positions of several groups of samples across all the components of an icaSet object.
● Data Source:
BioConductor
● Keywords: internal
● Alias: plotPosSamplesInComp
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plot_heatmapsOnSel
(Package: MineICA) :
Plot heatmap associated with each component
This function plots the heatmaps representing the measured values of the contributing features/genes on each component. It also plots the sample annotations above each heatmap using colours.
● Data Source:
BioConductor
● Keywords:
● Alias: plot_heatmapsOnSel
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qualVarAnalysis
(Package: MineICA) :
Tests association between qualitative variables and components.
This function tests if the groups of samples formed by the variables are differently distributed on the components, in terms of contribution value (i.e of values in matrix A(icaSet)). The distribution of the samples on the components are represented using either density plots of boxplots. It is possible to restrict the tests and the plots to a subset of samples and/or components.
● Data Source:
BioConductor
● Keywords:
● Alias: qualVarAnalysis
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quantVarAnalysis
(Package: MineICA) :
Correlation between variables and components.
This function tests if numeric variables are correlated with components.
● Data Source:
BioConductor
● Keywords:
● Alias: quantVarAnalysis
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