Nothing
## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.align = "center",
out.width = "100%",
fig.width = 9, fig.height = 7
)
## -----------------------------------------------------------------------------
set.seed(42)
library(NAIR)
dir_out <- tempdir()
toy_data <- simulateToyData()
head(toy_data)
## -----------------------------------------------------------------------------
nrow(toy_data)
## -----------------------------------------------------------------------------
net <- buildNet(toy_data, "CloneSeq")
## ----eval = FALSE-------------------------------------------------------------
# net <- buildNet(toy_data, "CloneSeq", min_seq_length = 10)
## ----eval = FALSE-------------------------------------------------------------
# net <- buildNet(toy_data, "CloneSeq", drop_matches = "\\W")
## ----eval = FALSE-------------------------------------------------------------
# net <- buildNet(toy_data, "CloneSeq", dist_type = "lev")
## ----eval = FALSE-------------------------------------------------------------
# net <- buildNet(toy_data, "CloneSeq", dist_cutoff = 0)
## ----eval = FALSE-------------------------------------------------------------
# net <- buildNet(toy_data, "CloneSeq", drop_isolated_nodes = FALSE)
## -----------------------------------------------------------------------------
net <- buildNet(toy_data, "CloneSeq", node_stats = TRUE)
## ----eval = FALSE-------------------------------------------------------------
# net <- buildNet(toy_data, "CloneSeq", cluster_stats = TRUE)
## -----------------------------------------------------------------------------
net <- buildNet(toy_data, "CloneSeq",
node_stats = TRUE,
color_nodes_by = c("SampleID", "transitivity", "coreness"),
color_scheme = c("default", "plasma-1", "mako-1"),
color_title = c("", "Transitivity", "Coreness"),
size_nodes_by = "degree",
node_size_limits = c(0.1, 1.5),
plot_title = NULL,
plot_subtitle = NULL,
print_plots = TRUE
)
## -----------------------------------------------------------------------------
names(net)
## -----------------------------------------------------------------------------
net$details
## -----------------------------------------------------------------------------
head(net$node_data)
## -----------------------------------------------------------------------------
names(net$plots)
## -----------------------------------------------------------------------------
class(net$plots$uniform_color)
## ----eval = FALSE-------------------------------------------------------------
# library(magrittr) # For pipe operator (%>%)
# toy_data %>%
# filterInputData("CloneSeq", drop_matches = "\\W") %>%
# buildNet("CloneSeq") %>%
# addNodeStats("all") %>%
# addClusterMembership("greedy", cluster_id_name = "cluster_greedy") %>%
# addClusterMembership("leiden", cluster_id_name = "cluster_leiden") %>%
# addClusterStats("cluster_leiden", "CloneSeq", "CloneCount") %>%
# addPlots(color_nodes_by = c("cluster_leiden", "cluster_greedy"),
# color_scheme = "Viridis"
# ) %>%
# labelClusters("cluster_leiden", cluster_id_col = "cluster_leiden") %>%
# labelClusters("cluster_greedy", cluster_id_col = "cluster_greedy") %>%
# saveNetwork(output_dir = tempdir(), output_name = "my_network")
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