chord_dat
(Package: GOplot) :
Creates a binary matrix.
The function creates a matrix which represents the binary relation (1= is related to, 0= is not related to) between selected genes (row) and processes (column). The resulting matrix can be visualized with the GOChord function.
● Data Source:
CranContrib
● Keywords:
● Alias: chord_dat
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GOCluster
(Package: GOplot) :
Circular dendrogram.
GOCluster generates a circular dendrogram of the data clustering using by default euclidean distance and average linkage.The inner ring displays the color coded logFC while the outside one encodes the assigned terms to each gene.
● Data Source:
CranContrib
● Keywords:
● Alias: GOCluster
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GOCircle
(Package: GOplot) :
Circular visualization of the results of a functional analysis.
The circular plot combines gene expression and gene- annotation enrichment data. A subset of terms is displayed like the GOBar plot in combination with a scatterplot of the gene expression data. The whole plot is drawn on a specific coordinate system to achieve the circular layout.The segments are labeled with the term ID.
● Data Source:
CranContrib
● Keywords:
● Alias: GOCircle
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GOHeat
(Package: GOplot) :
Displays heatmap of the relationship between genes and terms.
The GOHeat function generates a heatmap of the relationship between genes and terms. Biological processes are displayed in rows and genes in columns. In addition genes are clustered to highlight groups of genes with similar annotated functions. The input can be generated with the chord_dat function.
● Data Source:
CranContrib
● Keywords:
● Alias: GOHeat
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reduce_overlap
(Package: GOplot) :
Eliminates redundant terms.
The function eliminates all terms with a gene overlap >= set threshold (overlap) The reduced dataset can be used to improve the readability of plots such as GOBubble and GOBar
● Data Source:
CranContrib
● Keywords:
● Alias: reduce_overlap
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circle_dat
(Package: GOplot) :
Creates a plotting object.
The function takes the results from a functional analysis (for example DAVID) and combines it with a list of selected genes and their logFC. The resulting data frame can be used as an input for various ploting functions.
● Data Source:
CranContrib
● Keywords:
● Alias: circle_dat
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GOBar
(Package: GOplot) :
Z-score coloured barplot.
Z-score coloured barplot of terms ordered alternatively by z-score or the negative logarithm of the adjusted p-value
● Data Source:
CranContrib
● Keywords:
● Alias: GOBar
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The function creates a bubble plot of the input data. The input data can be created with the help of the circle_dat function.
● Data Source:
CranContrib
● Keywords:
● Alias: GOBubble
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GOChord
(Package: GOplot) :
Displays the relationship between genes and terms.
The GOChord function generates a circularly composited overview of selected/specific genes and their assigned processes or terms. More generally, it joins genes and processes via ribbons in an intersection-like graph. The input can be generated with the chord_dat function.
● Data Source:
CranContrib
● Keywords:
● Alias: GOChord
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GOVenn
(Package: GOplot) :
Venn diagram of differentially expressed genes.
The function compares lists of differentially expressed genes and illustrates possible relations.Additionally it represents the variety of gene expression patterns within the intersection in small pie charts with three segements. Clockwise are shown the number of commonly up- regulated, commonly down- regulated and contra- regulated genes.
● Data Source:
CranContrib
● Keywords:
● Alias: GOVenn
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