DEVis (version 1.0.1)

plot_mds: Visualize multi-dimensional scaled data for all samples, with group-wise metadata incorporated as colors and shapes.

Description

This function performs multi-dimensional scaling (MDS) on data to visualize levels of similarity between individual samples. Colors and shape variables can be specified according to available metadata, making it possible to identify patterns in the data based on groups. For instance, by coloring data points based on "Infected/Non-infected" groups, and drawing data point shapes based on time point, it is possible to view the differences between infected and non-infected samples across multiple time points.

Usage

plot_mds(filename = "mds_plot.pdf", color_var, shape_var = "none",
  showConf = TRUE, theme = 1, customLabels = FALSE,
  returnData = FALSE)

Arguments

filename

Filename for output plot. Valid extensions are ".pdf" and ".png". File generation for plot file can be turned off using set_output_mode("screen"). Output will be written to the /MDS/standard/ directory.

color_var

The group from target data that should be indicated by color. Any column of metadata can be used, regardless of experimental design.

shape_var

The group from target data that should be indicated by shape. Any column of metadata can be used, regardless of experimental design. (Optional). Default="none".

showConf

Boolean. Draw an ellipsis representing the 95 percent confidence interval around each group. Default: TRUE

theme

Theme for the layout and color scheme for the MDS 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

If this value is true, this function will return a sample distance matrix. Default: FALSE

Value

If returnData is true, this function will return a matrix containing sample distances computed to create the MDS plot.

See Also

plot_mds_hulls

Examples

# NOT RUN {
#These examples assume "Time" and "Infection" columns exist in target metadata.

#Make a MDS plot showing all samples, colored based on time point.
plot_mds(filename="mds_plot.pdf", color_var="Time", shape_var="none",
          theme=1, returnData=FALSE)

#Make a MDS plot, colored based on time point with shapes based on infection.
plot_mds(filename="mds_plot.pdf", color_var="Time", shape_var="Infection",
          theme=2, returnData=FALSE)

# }