Gene_Violin_plots: Gene Violin plot

In SaritaPoonia/unCTC: Characterising single circulating tumor cell transcriptomes

Gene Violin plot

Description

Create Violin plot of specific gene and compare expression in all data in data list.

Usage

Gene_Violin_plots(
  data_list = list(),
  data_id = list(),
  min_Sample = 5,
  min_Gene = 1500,
  gene_symbol = "",
  MetaData = list(),
  Groupby = "Clusters",
  DDLKCluster_data
)

Arguments

data_list	List of expression matricies
data_id	List of names/ids of expression matrix
min_Sample	gene filter, filter out genes which are not expressed in at least min_Sample cells
min_Gene	cell filter, filter out those cells which do not express at least min_Gene genes
gene_symbol	Gene should present in all expression data of data_list
MetaData	Optional, List of metadata of expression matricies in same order in which expression matricies in data_list, Column number and names of all the MetaData in the list must be same
Groupby	column name in MetaData according to which data is grouped.
DDLKCluster_data	PathwayDDLK_clust from DDLK_Clust.R method

Value

Violin_plot violin plot and plot object of given gene.

Examples

data1 = unCTC::Poonia_et_al._TPMData
data2 = unCTC::Ding_et_al._WBC1_TPMData
Data_list = list(data1,data2)
Data_Id = list("data1","data2")
Violin_plots = Gene_Violin_plots(data_list=Data_list,
                                 data_id= Data_Id,
                                 min_Sample = 5,
                                 min_Gene = 1500,
                                 Groupby = "data_id",
                                  gene_symbol ="TSPAN6" )

SaritaPoonia/unCTC documentation built on Nov. 8, 2022, 12:07 p.m.