Tjct.core.plot: Tjct.core.plot

In chenweng1991/EZsinglecell:

Usage

Tjct.core.plot(object = NULL, secondobj = NULL, pheno = NULL,
  f1.name = "XX.10d.violin.pdf", f2.name = "XX.his.pdf",
  f3.name = "XX.trj.heatmap.pdf", f3.height = 12,
  f3.tittle = "cell type:Changing genes on phenotype trajectory\ntop6%",
  table1.name = "XX.traj.up.genes-q0.05top0.06.csv",
  table2.name = "XX.traj.dowb.genes-q0.05top0.06.csv", rankcut = 0.06)

Arguments

object	The first trajectory generated by Prepareforpseudoregress.g
secondobj	The regressed and bined object by Tjct.core.gen
pheno	This is the column we are interested for RePACT gotta be the same with previous Prepareforpseudoregress.g
f1.name	The pdf name of violin plot "XX.10d.violin.pdf". 10 d means 10 PCs used.
f2.name	The pdf name of histgram "XX.his.pdf".
f3.name	The pdf name of the heatmap "XX.trj.heatmap.pdf".
f3.height	The pdf heigh for heatmap, change this when the number of genes shown is changed, default is 12
f3.tittle	The figure title for heatmap."cell type:Changing genes on phenotype trajectory\ntop6 \item table1.nameThe name of a csv file for upregulated genes"XX.traj.up.genes-q0.05top0.06.csv" \item table2.nameThe name of a csv file for upregulated genes"XX.traj.up.genes-q0.05top0.06.csv" \item rankcutThe percentile to be shown on the heatmap. default is 0.06

A list of upregulated and downregulated trajectory genes. This function is to generate major plots for Repact analysis Tjct.core.plot(BMI.tjct.ob,BMI.tjct.2nd.ob,pheno="BMI",f1.name="BMI.tjct.10d.violin.pdf",f2.name="BMI.tjct.his.pdf",f3.name="BMI.tjct.trj.heatmap.pdf",f3.height=14,f3.tittle="cell type:Changing genes on phenotype trajectory\ntop6%",table1.name="BMI.tjct.traj.up.genes-q0.05Full.csv",table2.name="BMI.tjct.traj.dowb.genes-q0.05Full.csv",rankcut=0.05)

chenweng1991/EZsinglecell documentation built on July 11, 2020, 3:23 p.m.