DEVis (version 1.0.1)

plot_group_stats: Visualize overall data set as a function of a metadata grouping.

Description

This function plots groupwise expression as with regard to a specified target data grouping. This function can be used to visualize the overall data set according to metadata grouping. For instance, overall expression at different timepoints can be viewed, or infected vs control expression levels can be plotted. This visualization is also ideal for examining the impact of normalization or filtering.

Usage

plot_group_stats(filename = "group_stats_plot.pdf", id_field, groupBy,
  normalized = TRUE, theme = 1, returnData = FALSE)

Arguments

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 /group_stats/ directory.

id_field

The unique ID field for this data set. Should be the field that corresponds to count column names and target rownames.

groupBy

The field by which to group samples in the boxplot. I.E. "time"

normalized

Toggles between whether normalized or non-normalized data should be used. Boolean. Default=TRUE.

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, log fold-change, and gene name.

Examples

# NOT RUN {
#Plot the overall data set expression levels grouped by time.
plot_group_stats("group_stats_plot.pdf", "SampleID", groupBy="Time",
                   normalized=TRUE, theme=1, returnData=FALSE)

# }