LRC3_CellTypeConnection: Visualize the connections for a specific cell type.

Description Usage Arguments

View source: R/LRC3_Alpha.R

Description

This function extracts and plots connections of a specific cell type with other cell types. For a certain cell type, ligand to receptor is defined as OUT signal and receptor to ligand is defined as IN signal. By setting parameters, users can chose the type of signals to view. The ligand-receptor pairs are ranked by their mean expression value.

Usage

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LRC3_CellTypeConnection(LRC3_list, CellType_Index = 1,
  By_Proportion = FALSE, Combine_InOut = FALSE, TargetCellType_IN = FALSE,
  TargetCellType_OUT = FALSE, ViewTop_LRpairs = FALSE, TOP_Number = 50,
  SaveImage = FALSE)

Arguments

LRC3_list

the input data generated by function LRC3_INF.

CellType_Index

the Index of the queried cell type that users are interested. The maximum number is the number of cell types.

By_Proportion

if By_Proportion = FALSE, view the connections based on the mean expression of cell types. if By_Proportion = TRUE, view the connections based on the proportion of cells within a cell type that significantly express the specific ligand or receptor.

Combine_InOut

If Combine_InOut = TRUE, it gives a figure that combines the IN and OUT signal tegether.

TargetCellType_IN

if TargetCellType_IN = TRUE,it shows the IN signal for the cell type in query.

TargetCellType_OUT

if TargetCellType_OUT = TRUE, it shows the OUT signal for the cell type in query.

ViewTop_LRpairs

if ViewTop_LRpairs = FALSE, show all the ligand-receptor pairs in the output figure. if ViewTop_UniqLRpairs = TRUE, show a number of top highly expressed ligand-receptor pairs in the output figure. The ligand-receptor pairs are ranked by their mean expression value in an decreasing order.

TOP_Number

the number of ligand-receptor pairs to show if ViewTop_LRpairs = TRUE.

SaveImage

if SaveImage = FALSE,plot without saving the figure. if SaveImage = TRUE,save the figure as pdf.


XiaojuanShen/LRC3 documentation built on May 25, 2019, 6:26 p.m.