DEVis (version 1.0.1)

de_volcano: Visualize the expression & significance of differentially expressed genes.

Description

This function generates a volcano plot that displays the relation between expression and p-value for all DE genes in a result set.

Usage

de_volcano(res_list, filename = "volcano_plot.pdf", lfc_thresh = -1,
  strict_scale = TRUE, num_columns = 3, 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/volcano/ directory.

lfc_thresh

Log2 fold change threshold for highlighting genes on the volcano plot.

strict_scale

Boolean. If this is true scales for all samples will be forced to be identical, otherwise scales will vary depending on the dispersion of the volcano plot for each individual sample.

num_columns

Number of columns to use in the grid layout. Default=3.

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 sample names, categorical grouping, and sample IDs.

Examples

# NOT RUN {
#Make a volcano plot highlighting DE genes above 1.5 LFC threshold.
de_volcano(result_list, filename="volcano.pdf", lfc_thresh=1.5, 
           strict_scale=TRUE, theme=1, returnData=FALSE)

# }