In mlizhangx/Network-Analysis-for-Repertoire-Sequencing-: Network Analysis of Immune Repertoire

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.align = "center", 
  out.width = "100%",
  fig.width = 9, fig.height = 7
)

Introduction

Customized visual plots of a network graph can be produced when calling buildRepSeqNetwork() and afterward using using addPlots().

Simulate Data for Demonstration

set.seed(42)
library(NAIR)
toy_data <- simulateToyData()

Producing Plots

With buildRepSeqNetwork()/buildNet()

buildRepSeqNetwork() automatically generates a plot of the network graph by default:

net <- buildNet(toy_data, "CloneSeq")
net$plots$uniform_color

With addPlots()

addPlots() can be used with the list returned by buildRepSeqNetwork() to generate additional plots of the network graph.

net <- addPlots(net, color_nodes_by = "SampleID")
net$plots$SampleID

Reproducibility of Graph Layout

When creating the initial plot for a network, the coordinate layout of the nodes is generated pseudo-randomly. Other plots created in the same call to buildRepSeqNetwork() and subsequent calls to addPlots() will use the same graph layout as the initial plot (compare the previous two plots).

Different calls to buildRepSeqNetwork(), however, can produce plots of the same network with different layouts (compare the previous plot and next plot). For this reason, it is recommended to use set.seed() before calling buildRepSeqNetwork(). This allows the same graph layout to be reproduced across multiple executions of the same code in which the initial plots are generated.

set.seed(42)
net <- buildNet(toy_data, "CloneSeq")

Node Colors {.tabset}

Color Nodes According to Metadata

The nodes in the graph can be colored according to available metadata. The color_nodes_by parameter accepts a character string naming the variable to use. This can be any variable present in the node metadata.

buildNet(toy_data, "CloneSeq", 
         color_nodes_by = "CloneCount",
         print_plots = TRUE
)

Node Color Scale

The color_scheme parameter accepts a character string naming a preset color scale to use when coloring the nodes. It accepts the following values:

• "default" for default ggplot2 colors
• One of the following color scales from the viridis package:
• "magma" (or "A")
• "inferno" (or "B")
• "plasma" (or "C")
• "viridis" (or "D")
• "cividis" (or "E")
• "rocket" (or "F")
• "mako" (or "G")
• "turbo" (or "H")
• Any of the above viridis color scales with "-1" appended (e.g., "mako-1"), which reverses the direction of the color scale
• If the variable is discrete, a color palette from grDevices::hcl.pals() (e.g., "RdBu")

net <- buildNet(toy_data, "CloneSeq", 
                node_stats = TRUE,
                color_nodes_by = "transitivity", 
                color_scheme = "plasma-1",
                print_plots = TRUE
)

Custom Color Scales {.tabset}

The color scales that are available through the color_scheme parameter are limited to a selection of preset color scales. A customized color scale can be applied to the plot after it is created.

If the variable used to color the nodes is continuous, a custom two-color gradient can be applied using ggplot2::scale_color_gradient().

net$plots$transitivity <- net$plots$transitivity +
  ggplot2::scale_color_gradient(low = "pink", high = "purple4")

net$plots$transitivity  

Similarly, ggplot2::scale_color_gradient2() can be used to apply a three-color diverging gradient.

If the variable used to color the nodes is discrete, a custom color palette can be applied using the ggplot2::scale_color_manual() function, which allows the user to specify the color used for each value. The parameter values accepts a vector of colors whose length matches the number of unique values.

# Sample ID is a discrete variable
net <- addPlots(net, color_nodes_by = "SampleID")

net$plots$SampleID <- net$plots$SampleID + 
  ggplot2::scale_color_manual(values = c("deepskyblue", "red2"))

net$plots$SampleID

Node Size {.tabset}

By default, all nodes are drawn using a uniform size value of 0.5. This value is suitable for large networks with many nodes.

The node size can be specified by providing a positive value to the size_nodes_by parameter.

net <- addPlots(net,
                color_nodes_by = "transitivity", 
                color_scheme = "plasma-1",
                size_nodes_by = 1.5,
                print_plots = TRUE
)

Size Nodes According to Metadata

The nodes can be sized dynamically according to a variable in the node metadata. The size_nodes_by parameter accepts a character string naming the variable.

The node size scale can be adjusted using the node_size_limits parameter, which accepts a numeric vector of length two specifying the minimum and maximum node size.

net <- addPlots(net,
                color_nodes_by = "transitivity", 
                color_scheme = "plasma-1",
                size_nodes_by = "degree", 
                node_size_limits = c(0.1, 2.5),
                print_plots = TRUE
)

Text Elements {.tabset}

This section covers parameters that control text elements in the plot, such as titles, annotations and legends.

Title and Subtitle

The default title for plots created by buildRepSeqNetwork() is the argument value to the output_name parameter ("MyRepSeqNetwork" by default). Plots created by addPlots() have no default title.

For both buildRepSeqNetwork() and addPlots(), the default subtitle includes information about the network's construction, such as the values of dist_type and dist_cutoff.

A custom plot title and subtitle can be provided as character strings to the plot_title and plot_subtitle parameters. An argument value of NULL omits the corresponding element from the plot.

net <- addPlots(
  net,
  plot_title = "Immune Repertoire Network by TCR Sequence Similarity",
  plot_subtitle = NULL
)

Legends {.tabset}

Hiding Legends

By default, if the nodes are colored or sized dynamically according to a variable, a legend will be included in the plot showing the color scale and/or size scale.

The color scale legend can be hidden using color_legend = FALSE. Similarly, size_legend = FALSE hides the size scale legend.

Note: When the variable used to color the nodes is discrete with more than 20 distinct values, the color scale is automatically excluded from the legend to prevent it from crowding the plot. The name of the node color variable is then appended to the plot's subtitle. To force the color legend to be shown, use color_legend = TRUE.

Legend Titles

The default titles of the color and size scales are the names of the variables used to color and size the nodes. Custom titles can be provided as character strings to the color_title and size_title parameters. An argument value of NULL or "" omits the title.

If a vector is provided to the color_nodes_by parameter in order to generate multiple plots, then the color_title accepts a character vector of matching length, where each entry is the title for the color legend in the corresponding plot.

Labeling Clusters

After performing cluster analysis, it can be helpful to label clusters in the plot with their cluster IDs for reference, as shown here.

Labeling Nodes

addGraphLabels() can be used to label individual nodes.

Generating Multiple Plots

buildRepSeqNetwork() and addPlots() can generate multiple plots in a single call, with each plot coloring the nodes according to a different variable. The color_nodes_by parameter accepts a character vector naming the variables to use. The color_scheme parameter will accept a character vector of matching length specifying the color scale for each plot, or a character string specifying a single color scale to use in all plots.

net <- addPlots(net,
                color_nodes_by = c("coreness", "degree"),
                color_scheme = c("plasma-1", "mako-1"),
                color_title = c("Coreness", "Network Degree"),
                size_title = "Network Degree",
                size_nodes_by = "degree", 
                node_size_limits = c(0.1, 1.5),
                plot_subtitle = NULL,
                print_plots = TRUE
)

Saving Plots

After adding or modifying plots in the list of network objects, the list of network objects can be saved using saveNetwork(), which also prints the plots to a PDF. saveNetworkPlots() saves the PDF only.

saveNetwork(net, output_dir = dir_out)

saveNetworkPlots(net$plots, outfile = file.path(dir_out, "plots.pdf"))

mlizhangx/Network-Analysis-for-Repertoire-Sequencing- documentation built on April 7, 2024, 12:02 p.m.