de_diverge_plot: Visualize fold-change divergence for differentially expressed...

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

Description

This function plots the log2 fold-change values for all differentially expressed genes for each contrast in a result set. This plot visualizes the distribution and strength of expression changes for all differentially expressed genes.

Usage

de_diverge_plot(res_list, filename = "de_divergence_plot.pdf",
  theme = 1, customLabels = FALSE, 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/divergence/ directory.
theme	Theme for the layout and color scheme for the plot. Valid selections are integers between 1-6.
customLabels	If customLabels is set to TRUE, the user will be prompted to provide a custom label for each label.
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 for differentially expressed genes containing gene names, categorical variable, and expression values.

Examples

## Not run: 

#Prepare a result list.
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)

#Create the plot.
de_diverge_plot(res_list=myResList, filename="DE_divergence_plot.pdf",
                 theme=1, returnData=FALSE)


## End(Not run)

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