obtainMarkersWCScran: obtainMarkersWCScran

In noriakis/wcGeneSummary: visualization and interpretation of textual information from omics summary data through network analysis

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.