color_code_node_2: color_code_node_2 plot state transition network in which...

In dynverse/Mpath: Mpath: a single-cell RNAseq data analysis algorithm that maps multi-branching single-cell trajectories revealing cell progression during development

Description

color_code_node_2 plot state transition network in which nodes i.e. landmarks are color-coded by average expression of the given gene

Usage

color_code_node_2(networkFile, rpkmFile, lmFile, geneName, baseName = NULL,
  seed = NULL)

Arguments

networkFile	a tab delimited file containing a matrix of trimmed state transition network, column and row names are landmarks, the values are 0 or 1 indicating whether the two landmarks are connected.
rpkmFile	a tab delimited txt file of expression data, containing cells in columns and genes in rows
lmFile	a tab delimited file of landmark cluster assignment of individual cells. The first column indicates cell ID, the second column indicates the landmark cluster which the cell was assigned to.
geneName	gene name or a vector of gene names
baseName	prefix name of resulting files
seed	the seed

Examples

## Not run: 
rpkmFile="TPM_GSE60783_noOutlier.txt";
lmFile="TPM_GSE60783_noOutlier_geneQC0.05anyGroup_CD4vsCD8DEG_landmark_cluster.txt";
network="TPM_GSE60783_noOutlier_geneQC0.05anyGroup_CD4vsCD8DEG_state_transition_mst.txt";
# network can be the return value of trim_net 
color_code_node_2(networkFile=network,
                  rpkmFile=rpkmFile,
                  lmFile=lmFile,
                  geneName=c("Irf8","Id2","Batf3"),
                  baseName="cDC1_marker",
                  seed=NULL)

## End(Not run)

dynverse/Mpath documentation built on May 14, 2019, 8:42 a.m.