# Plot TSSs and clusters

`plotTSS.Rd`

Plots Gviz-track of TSSs, clusters, and genes.

    plotTSS(object,samples,tssData = "processed",clusters = "assigned",
    clusterThreshold = 0.02,genelist,Bidirection = TRUE,up.dis =500,down.dis = 500)

    # S4 method for TSSr
    plotTSS(
      object,
      samples,
      tssData = "processed",
      clusters = "assigned",
      clusterThreshold = 0.02,
      genelist,
      Bidirection = TRUE,
      up.dis = 500,
      down.dis = 500
    )

## Arguments

object | A TSSr object.
samples | Specify samples to be included for plotting.
tssData | Specify which TSS data to be included for plotting: "raw" or "processed".
clusters | Specify which cluster data to be included for plotting: "all" or "assigned".
clusterThreshold | Ignore downstream clusters if signal < filterClusterThreshold*the strongest clusters within the same gene promoter region. Default value = 0.02.
genelist | List of gene names used for plotting.
Bidirection | Specify whether to display bidirectional TSS signals within defined region. Default is TRUE.
up.dis | Distance upstream of genes to specify plotting range. Default value = 500.
down.dis | Distance downstream of genes to specify plotting range. Default value = 500.

## Examples

    # \donttest{
    plotTSS(exampleTSSr, samples=c("control","treat"), genelist=c("YBL017C","YBL067C")
    ,up.dis =500, down.dis = 500)#> Plotting TSS graphs...#> Import genomic features from the file as a GRanges object ... #> Error in open.connection(con, open): cannot open the connection# }