obtainMarkersWCScran: obtainMarkersWCScran

View source: R/geom_sc_wordcloud.R

obtainMarkersWCScranR Documentation

obtainMarkersWCScran

Description

Make gene wordcloud from scran::findMarkers() results

Usage

obtainMarkersWCScran(
  markers,
  cols,
  wcArgs,
  eps = 1e-10,
  sortBy = "summary.logFC",
  decreasing = TRUE,
  scaleNumber = 10,
  wcScale = 5,
  geneNum = 50,
  withggfx = NULL,
  ggfxParams = list()
)

Arguments

markers

marker list

cols

list of colors

wcArgs

arguments for ggwordcloud

eps

when taking log of p-values, this value will be added

sortBy

default to summary.logFC, "log10p" can be specified.

decreasing

sort by decreasing order or not

scaleNumber

scale the frequency by this number

wcScale

scale for scale_size_area()

geneNum

number of genes to be included in wordclouds

withggfx

applying ggfx filters

ggfxParams

parameter list for ggfx

Details

using the results of marker gene identification such as 'findMarkers' from scran, Recursively summarize the textual information of markers and output the wordclouds.

Value

list of ggplot containing wordclouds

Examples

df <- data.frame(
  p.value=c(0.01, 0.01),gene=c("PNKP","DDX41")
)
row.names(df) <- df$gene
markers <- list("1"=df)
colors <- list("1"="blue")
obtainMarkersWCScran(markers,
                     cols=colors,
                     wcArgs=list(),
                     sortBy="p.value",
                     geneNum=2)

noriakis/wcGeneSummary documentation built on May 31, 2024, 4:42 p.m.