TextMarkers: TextMarkers

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

TextMarkers

Description

Take results of 'Seurat::FindAllMarkers' as input and plot wordcloud or network for all the clusters.

Usage

TextMarkers(
  df,
  keyType = "SYMBOL",
  type = "wc",
  genePlot = TRUE,
  genePlotNum = 5,
  colorText = TRUE,
  args = list(),
  wcArgs = NULL,
  raw = FALSE,
  col = NULL,
  pvalThresh = 0.05,
  withTitle = TRUE,
  withggfx = NULL,
  ggfxParams = list()
)

Arguments

df	result of FindAllMarkers()
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, named list of clusters
pvalThresh	adjusted p-value threshold for markers
withTitle	plot title on the plot
withggfx	applying ggfx filters
ggfxParams	parameter list for ggfx

Details

Using the results of marker gene identification such as 'FindAllMarkers' from Seurat, Recursively summarize the textual information of markers and output the visualizations.

Value

list of plots on textual information in the gene cluster

See Also

obtainMarkersWC

Examples

markers <- data.frame(p_val_adj=c(0.01, 0.01, 0.04),
gene=c("PNKP","DDX41","IRF3"),cluster=c("1","1","1"))
colors <- list("1"="red")
TextMarkers(markers, col=colors, type="wc")

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