cytofkit (version 1.4.4)

cytof_progressionPlot: Progression plot

Description

Plot the expression trend along the estimated cell progressing order

Usage

cytof_progressionPlot(data, markers, orderCol = "isomap_1",
  clusterCol = "cluster", min_expr = NULL,
  trend_formula = "expression ~ sm.ns(Pseudotime, df=3)")

Arguments

data

The data frame for progression plot.

markers

The column names of the selected markers for visualization.

orderCol

The column name of the estimated cell progression order.

clusterCol

The column name of the cluster results

min_expr

the threshold of the minimal expression value for markers

trend_formula

a symbolic description of the model to be fit.

Value

• a heatmap object from gplots

Examples

m1 <- c(rnorm(300, 10, 2), rnorm(400, 4, 2), rnorm(300, 7))
m2 <- c(rnorm(300, 4), rnorm(400, 16), rnorm(300, 10, 3))
m3 <- c(rnorm(300, 16), rnorm(400, 40, 3), rnorm(300, 10))
m4 <- c(rnorm(300, 7, 3), rnorm(400, 30, 2), rnorm(300, 10))
m5 <- c(rnorm(300, 27), rnorm(400, 40, 1),rnorm(300, 10))
c <- c(rep(1,300), rep(2,400), rep(3,300))
rnames <- paste(paste('sample_', c('A','B','C','D'), sep = ''), 
rep(1:250,each = 4), sep='_') 
exprs_cluster <- data.frame(cluster = c, m1 = m1, m2 = m2, m3 = m3, m4 = m4, isomap_1 = m5)
row.names(exprs_cluster) <- sample(rnames, 1000)
cytof_progressionPlot(exprs_cluster, markers = c("m1","m2","m3","m4"))