density_points

density_points

density_points(
  meta_data,
  cluster_list = NULL,
  method = "combine",
  celltype_by = NULL,
  group_column = "cluster",
  pseudotime_column = "pseudotime",
  min_cells = 100,
  plot = FALSE,
  key_word = "network_",
  key_sign = "..",
  file_save = NULL,
  color_list = c("#0066ff", "#0099ff", "#66cc33", "#66ff33", "#ccff00", "#ffff99",
    "#ffff33", "#ffcc33", "#ff9933", "#ff6633", "#cc3300", "#ff3333")
)

Arguments

meta_data

meta_data

cluster_list

cluster_list

method

method

celltype_by

celltype_by

group_column

group_column

pseudotime_column

pseudotime_column

min_cells

min_cells

plot

plot

key_word

key_word

key_sign

key_sign

file_save

file_save

color_list

color_list

Value

points

Examples

test_data <- rbind(
  data.frame(
    cluster = "cluster1",
    pseudotime = rnorm(500, mean = 1, sd = 1)
  ),
  data.frame(
    cluster = "cluster2",
    pseudotime = rnorm(500, mean = 2, sd = 2)
  ),
  data.frame(
    cluster = "cluster3",
    pseudotime = rnorm(500, mean = 3, sd = 3)
  )
)

density_points(
  meta_data = test_data,
  plot = TRUE
)

#>      window cluster1 cluster2 time_point1 time_point2
#> 1 network_1 cluster1 cluster3   0.9253374    2.238531
#> 2 network_2 cluster3 cluster2   2.2385311    2.446525

density_points(
  meta_data = test_data,
  cluster_list = list(c("cluster1", "cluster3")),
  plot = TRUE,
  color_list = c("#ff0000", "#ffcc00")
)

#>      window cluster1 cluster2 time_point1 time_point2
#> 1 network_1 cluster1 cluster3   0.9253374    2.238531

density_points(
  meta_data = test_data,
  method = "intersection",
  plot = TRUE
)

#>      window cluster1 cluster2 time_point1 time_point2
#> 1 network_1 cluster1 cluster2   -5.847251   -1.152391
#> 2 network_2 cluster1 cluster2    2.582157   12.327548