de_boxplot: Visualize differentially expressed genes as a function of...

In DEVis: A Differential Expression Analysis Toolkit for Visual Analytics and Data Aggregation

Description

This function plots groupwise expression for all differentially expressed genes with regard to the experimental design. For example, for a differential expression design of ~Condition_Time, boxplots for differentially expressed genes for each condition_time case in the targets metadata will be produced.

Usage

de_boxplot(res_list, filename = "de_boxplot.pdf", theme = 1,
  returnData = FALSE)

Arguments

res_list	A list of DESeq result sets. Results can be calculated individually using DESeq's results() function. Lists of results can be created by creating a list(result1, result2 ... result_N).
filename	Filename for output plot. Valid extensions are ".pdf" and ".png". File generation can be turned off using set_output_mode("screen"). Output will be written to the /DE/boxplot/ directory.
theme	Theme for the layout and color scheme for the plot. Valid selections are integers between 1-6.
returnData	Boolean. Determines if this visualization should return data used to generate the visualization. Default=FALSE.

Value

If returnData is true, this function will return the long-form table of expression containing categorical grouping, and sample IDs, and log2 fold-change.

Examples

## Not run: 

#Prepare a result list for aggregation.
res.day1 <- results(dds, contrast=c("Condition_Time", "day1_disease", "day1_control"))
res.day2 <- results(dds, contrast=c("Condition_Time", "day2_disease", "day2_control"))
res.day3 <- results(dds, contrast=c("Condition_Time", "day3_disease", "day3_control"))
myResList <- list(res.day1, res.day2, res.day3)

#Plot differentially expressed genes for the aggregate result sets.
de_boxplot(res_list=myResList, filename="DE_condition_time_boxplot.pdf",
            theme=2, returnData=FALSE)


## End(Not run)

DEVis documentation built on May 2, 2019, 3:18 p.m.