genecircosPlot: genecircosPlot Function

In aifimmunology/PALMO: Identify Intra and Inter-Donor Variations in Bulk or Single Cell Longitudinal Dataset

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.