PALMO (version 0.1.2)

genecircosPlot: 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
)

Value

Circos plots and dataframe

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).

Examples

if (FALSE) {
genecircosPlot(data_object=palmo_obj, geneList=c('IL32','CCL5','TCF7'))
}