TextMarkersScran: TextMarkersScran

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

TextMarkersScran

Description

Make gene wordcloud from scran::findMarkers() results

Usage

TextMarkersScran(
  res,
  keyType = "SYMBOL",
  type = "wc",
  genePlot = TRUE,
  genePlotNum = 5,
  colorText = TRUE,
  args = list(),
  wcArgs = NULL,
  raw = FALSE,
  col = NULL,
  withTitle = TRUE,
  top = 5,
  withggfx = NULL,
  FDRThresh = 0.05,
  ggfxParams = list()
)

Arguments

res	result of findMarkers()
keyType	keytype
type	wc or network
genePlot	whether to plot relevant genes
genePlotNum	number of genes to plot
colorText	colorlize text or not, default to TRUE
args	parameters to pass to refseq
wcArgs	parameters to pass to ggwordcloud
raw	obtain raw results of refseq instead of plot
col	color to be used in wordcloud
withTitle	ggtitle(cluster name) will be added
top	Top-top genes for each cluster will be included
withggfx	applying ggfx filters
FDRThresh	FDR threshold
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 visualizations.

Value

list of ggplot

See Also

obtainMarkersWCScran

Examples

df <- data.frame(
  p.value=c(0.01, 0.01),gene=c("PNKP","DDX41"),
  Top=c(1,2),FDR=c(0.01, 0.01)
)
row.names(df) <- df$gene
markers <- list("1"=df)
colors <- list("1"="blue")
TextMarkersScran(markers, col=colors)

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