de_counts: Visualize differentially expressed gene counts as a stacked...

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

Description

This function generates a stacked barplot representing differentially expressed gene counts for a result sets, distinguishing up and down regulated genes across one or more result sets. This function will produce a stacked barplot and an output file containing count information. Count data for the provided result sets will also be returned by this function.

Usage

de_counts(res_list, filename = "de_count_barplot.pdf",
  lfc_filter = FALSE, customLabels = FALSE, theme = 1,
  returnData = FALSE)

Arguments

res_list	A list of DESeq result sets created with DESeq2::results(). I.E: list(res1, res2, ..., resN).
filename	Output file destination. String. Valid extensions are .pdf and .png. The data file accompanying this plot file will have the same name, but will be output as a tab-delimited text file. Output will be written to the /DE/counts/ directory. Alternatively, file generation can be turned off using set_output_mode("screen").
lfc_filter	Boolean. Determines if DE counts should be displayed with or without the application of the log2FoldChange filter.
customLabels	If customLabels is set to TRUE, the user will be prompted to provide a custom label for each label on the x-axis.
theme	The color and design scheme for the output 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

A data frame containing count information for both up and down regulated gene counts for each result set provided in res_list. Output files will be written to /DE/counts/.

See Also

create_dir_struct, set_output_mode

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)

#Visualize count data for the result set and save the results.
de_counts(res_set=myResList, filename="DE_counts.png", theme=2)


## End(Not run)

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