genecircosPlot: genecircosPlot Function

View source: R/genecircosPlot.R

genecircosPlotR Documentation

genecircosPlot Function

Description

This function allows to Circos Plot for gene list of interest by group

Usage

genecircosPlot(
  data = NULL,
  data_object = NULL,
  geneList,
  group_position = 1,
  group_oi = NULL,
  titleName = "",
  colorThreshold = 10,
  colorMax = NULL,
  colorscale = FALSE
)

Arguments

data

Expression matrix or data frame. Rows represents gene/proteins column represents group:donor (or donor:group)

data_object

Input PALMO S4 object. It contains annotation information and expression data from Bulk or single cell data. Rows represents gene/proteins column represents group:donor (or donor:group)

geneList

User-defined genes of interest

group_position

Default 1, use 2 when columns are donor:group format

group_oi

Optional, User-defined groups to consider and order plot

titleName

Title of the plot

colorThreshold

User-defined color threshold (same as cvThreshold, like 5)

colorMax

Maximum CV value in heatplot ("max", numeric or NULL)

colorscale

Show color scale, TRUE or FALSE (default).

Value

Circos plots and dataframe

Examples

## Not run: 
genecircosPlot(data_object=palmo_obj, geneList=c('IL32','CCL5','TCF7'))

## End(Not run)

aifimmunology/PALMO documentation built on Oct. 21, 2022, 7:39 p.m.