PlotCategoryExpr: Plot the Expression Levels of each Age or Divergence Category as Boxplot, Violinplot, or Dotplot

Description

This function visualizes the expression level distribution of each phylostratum during each time point or experiment as boxplot, dot plot, or violin plot enabling users to quantify the age (PS) or divergence (DS) category specific contribution to the corresponding transcriptome.

Usage

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PlotCategoryExpr(ExpressionSet, legendName, test.stat = TRUE,
  type = "category-centered", distr.type = "boxplot", log.expr = FALSE,
  gene.set = NULL)

Arguments

ExpressionSet

a standard PhyloExpressionSet or DivergenceExpressionSet object.

legendName

a character string specifying whether "PS" or "DS" are used to compute relative expression profiles.

test.stat

a logical value indicating whether a Benjamini-Hochberg adjusted kruskal.test should be applied to determine significant differences in age or divergence category specific expression.

type

type of age or divergence category comparison. Specifications can be type = "category-centered" or type = "stage-centered".

distr.type

format of visualizing age or divergence category specific expression distributions. Either distr.type = "boxplot", distr.type = "dotplot", or distr.type = "violin".

log.expr

a logical value specifying whether or not expression levels should internally be log2-transformed before visualization.

gene.set

a character vector storing the gene ids for which gene expression levels shall be visualized.

Details

This way of visualizing the gene expression distribution of each age (PS) or divergence (DS) category during all developmental stages or experiments allows users to detect specific age or divergence categories contributing significant levels of gene expression to the underlying biological process (transcriptome).

This quantification allows users to conclude that genes originating in specific PS or DS contribute significantly more to the overall transcriptome than other genes originating from different PS or DS categories. More specialized analyses such as PlotMeans, PlotRE, PlotBarRE, etc. will then allow to study the exact mean expression patterns of these age or divergence categories.

The statistical quantification of differences between expression levels of different age or divergence categories is done by performing a kruskal.test with Benjamini & Hochberg p-value adjustment for multiple comparisons.

Argument Specifications:

Argument: type

Argument: distr.type

Finally, users can specify a gene.set (a subset of genes included in the input ExpressioSet) for which expression levels should be visualized as boxplot, dotplot, or violinplot.

Value

A boxplot, violin plot, or dot plot visualizing the gene expression levels of different PS or DS categories.

Furthermore, the statistical test results returned from the kruskal.test are printed to the console.

(1) '*' = P-Value <= 0.05

(2) '**' = P-Value <= 0.005

(3) '***' = P-Value <= 0.0005

(4) 'n.s.' = not significant = P-Value > 0.05

Author(s)

Hajk-Georg Drost

See Also

PlotMeans, PlotRE, PlotBarRE, age.apply, pTAI, pTDI, pStrata, pMatrix, TAI, TDI

Examples

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data(PhyloExpressionSetExample)
data(DivergenceExpressionSetExample)

## Not run: 

# category-centered visualization of PS specific expression level distributions (log-scale)
PlotCategoryExpr(ExpressionSet = PhyloExpressionSetExample,
                     legendName    = "PS",
                     test.stat     = TRUE,
                     type          = "category-centered",
                     distr.type    = "boxplot",
                     log.expr      = TRUE)
                     

# stage-centered visualization of PS specific expression level distributions (log-scale)
PlotCategoryExpr(ExpressionSet = PhyloExpressionSetExample,
                     legendName    = "PS",
                     test.stat     = TRUE,
                     distr.type    = "boxplot",
                     type          = "stage-centered",
                     log.expr      = TRUE)

                     
                                                               
# category-centered visualization of PS specific expression level distributions (log-scale)
# as violoin plot
PlotCategoryExpr(ExpressionSet = PhyloExpressionSetExample,
                     legendName    = "PS",
                     test.stat     = TRUE,
                     distr.type    = "violin",
                     type          = "stage-centered",
                     log.expr      = TRUE)




# analogous for DivergenceExpressionSets
PlotCategoryExpr(ExpressionSet = DivergenceExpressionSetExample,
                     legendName    = "DS",
                     test.stat     = TRUE,
                     type          = "category-centered",
                     distr.type    = "boxplot",
                     log.expr      = TRUE)


# visualize the expression levels of 500 example genes
set.seed(234)
example.gene.set <- PhyloExpressionSetExample[sample(1:25260,500) , 2]

PlotCategoryExpr(ExpressionSet = PhyloExpressionSetExample,
                 legendName    = "PS",
                 test.stat     = TRUE,
                 type          = "category-centered",
                 distr.type    = "boxplot",
                 log.expr      = TRUE,
                 gene.set      = example.gene.set)
                 

## End(Not run)

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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