Seurat feature plot

create and save a nice Seurat feature plot in folder featureplot

Usage

fPlot(
  path,
  object,
  par,
  reduction,
  width = 16,
  height = ceiling(length(genes_found)/4) * 3,
  order,
  dir_output = "."
)

Arguments

path

path to markers.csv

object

Seurat object

par

column name in markers.csv

reduction

a character string specifying the dimension reduction

width

width of output plot (default: 16)

height

height of output plot (default: length of genes divided by four, ceiling, times three)

order

should the feature plot be ordered in order of expression

dir_output

directory to save the output plot (default: ".")

Value

save feature plot

Examples

library(Seurat)
markers <- data.frame(B = c("MS4A1", "CD79A"))
write.csv(markers, "markers.csv")
fPlot(
  path = "markers.csv",
  object = pbmc_small,
  par = "B",
  reduction = "tsne",
  order = TRUE,
  dir_output = "."
)
#> New names:
#> • `` -> `...1`
#> Rows: 2 Columns: 2
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: ","
#> chr (1): B
#> dbl (1): ...1
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.

unlink("markers.csv")
unlink("fp_pbmc_small_B.png")