cytofkit (version 1.4.8)

cytof_progressionPlot: Progression plot

Description

Plot the expression trend along the estimated cell progressing order

Usage

cytof_progressionPlot(data, markers, clusters, orderCol = "isomap_1", clusterCol = "cluster", reverseOrder = FALSE, addClusterLabel = TRUE, clusterLabelSize = 5, segmentSize = 0.5, 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.

clusters

Selecte clusters for plotting, defauls select all.

orderCol

The column name of the estimated cell progression order.

clusterCol

The column name of the cluster results.

reverseOrder

If reverse the value of orderCol.

addClusterLabel

If add the cluster label on the plot.

clusterLabelSize

The size of the cluster label.

segmentSize

The size of the cluster label arrow.

min_expr

the threshold of the minimal expression value for markers.

trend_formula

a symbolic description of the model to be fit.

Value

a ggplot2 object

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"))