Plot rank density

Show the rank density of given signature in the given comparison.

sig_rankdensity_plot(
  data,
  sigs,
  group_col,
  aggregate = FALSE,
  slot = "counts",
  gene_id = "SYMBOL"
)

# S4 method for matrix,vector,vector
sig_rankdensity_plot(
  data,
  sigs,
  group_col,
  aggregate = FALSE,
  gene_id = "SYMBOL"
)

# S4 method for Matrix,vector,vector
sig_rankdensity_plot(
  data,
  sigs,
  group_col,
  aggregate = FALSE,
  gene_id = "SYMBOL"
)

# S4 method for data.frame,vector,vector
sig_rankdensity_plot(
  data,
  sigs,
  group_col,
  aggregate = FALSE,
  gene_id = "SYMBOL"
)

# S4 method for DGEList,vector,character
sig_rankdensity_plot(
  data,
  sigs,
  group_col,
  aggregate = FALSE,
  slot = "counts",
  gene_id = "SYMBOL"
)

# S4 method for ExpressionSet,vector,character
sig_rankdensity_plot(
  data,
  sigs,
  group_col,
  aggregate = FALSE,
  gene_id = "SYMBOL"
)

# S4 method for Seurat,vector,character
sig_rankdensity_plot(
  data,
  sigs,
  group_col,
  aggregate = FALSE,
  slot = "counts",
  gene_id = "SYMBOL"
)

# S4 method for SummarizedExperiment,vector,character
sig_rankdensity_plot(
  data,
  sigs,
  group_col,
  aggregate = FALSE,
  slot = "counts",
  gene_id = "SYMBOL"
)

# S4 method for list,vector,character
sig_rankdensity_plot(
  data,
  sigs,
  group_col,
  aggregate = FALSE,
  slot = "counts",
  gene_id = "SYMBOL"
)

Arguments

data

expression data, can be matrix, DGEList, eSet, seurat, sce...

sigs

a vector of signature (Symbols)

group_col

character or vector, specify the column name to compare in coldata

aggregate

logical, if to aggregate expression according to group_col, default FALSE

slot

character, indicate which slot used as expression, optional

gene_id

character, indicate the ID type of rowname of expression data's , could be one of 'ENSEMBL', 'SYMBOL', ... default 'SYMBOL'

Value

ggplot or patchwork

Examples

data("im_data_6", "nk_markers")
sig_rankdensity_plot(
  data = im_data_6, sigs = nk_markers$HGNC_Symbol[1:10],
  group_col = "celltype:ch1", gene_id = "ENSEMBL"
)
#> 'select()' returned 1:many mapping between keys and columns