plot_dendro: Create dendrograms based on hierarchical clustering.

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

Description

This function plots a dendrogram for the dataset as a whole using hierarchical clustering. Metadata can be applied to the dendrogram to examine how data cluster by different conditions. By examining how data cluster, it is possible to identify patterns in the data and batch effects. For example, creating a dendrogram that is grouped by the "case" condition in a case vs control experiment, it would be possible to identify a strong effect in the overall dataset between the case and control condition if most of the "case" conditions clustered strongly together. Batch effects can also be identified in this way. For instance, if samples were prepared at two different locations and this information was incorporated into the metadata as a "batch" column, visualizing the data based on batch data could indicate whether or not differences in the data are due to differences in the sample prep location, rather than due to a biological effect, depending on how strongly the batches cluster.

Usage

plot_dendro(filename = "dendro_plot.pdf", id_field, groupBy)

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 /dendrograms/ directory.
id_field	The unique sample ID field for your data. Should correspond to a column in targets data.
groupBy	A field in target meta data that you wish to cluster data by.

Value

This function does not return a value.

Examples

## Not run: 

#Plot a dendrogram based on an "infection" metadata field.
plot_dendro(filename="infection_dendro.pdf", "sample_id", "infection")

#Plot a dendrogram based on an "batch" metadata field.
plot_dendro(filename="batch_dendro.pdf", "sample_id", "batch")


## End(Not run)

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