plotCount: plotCount

In ruqianl/comapr: Crossover analysis and genetic map construction

plotCount

Description

Plot the number of COs per sample group or per chromosome

Usage

plotCount(
  co_count,
  by_chr = FALSE,
  group_by = "sampleGroup",
  plot_type = "error_bar"
)

## S4 method for signature 'RangedSummarizedExperiment,missing,missing'
plotCount(
  co_count,
  by_chr = FALSE,
  group_by = "sampleGroup",
  plot_type = "error_bar"
)

## S4 method for signature 'RangedSummarizedExperiment,missing,character'
plotCount(
  co_count,
  by_chr = FALSE,
  group_by = "sampleGroup",
  plot_type = "error_bar"
)

## S4 method for signature 'RangedSummarizedExperiment,logical,character'
plotCount(
  co_count,
  by_chr = FALSE,
  group_by = "sampleGroup",
  plot_type = "error_bar"
)

## S4 method for signature 'RangedSummarizedExperiment,logical,missing'
plotCount(
  co_count,
  by_chr = FALSE,
  group_by = "sampleGroup",
  plot_type = "error_bar"
)

## S4 method for signature 'GRanges,logical,missing'
plotCount(
  co_count,
  by_chr = FALSE,
  group_by = "sampleGroup",
  plot_type = "error_bar"
)

## S4 method for signature 'GRanges,missing,missing'
plotCount(
  co_count,
  by_chr = FALSE,
  group_by = "sampleGroup",
  plot_type = "error_bar"
)

## S4 method for signature 'GRanges,missing,character'
plotCount(
  co_count,
  by_chr = FALSE,
  group_by = "sampleGroup",
  plot_type = "error_bar"
)

## S4 method for signature 'GRanges,logical,character'
plotCount(
  co_count,
  by_chr = FALSE,
  group_by = "sampleGroup",
  plot_type = "error_bar"
)

Arguments

co_count	GRange or RangedSummarizedExperiment object, returned by countCO
by_chr,	whether it should plot each chromosome separately
group_by,	the column name in 'colData(co_count)' that specify the grouping factor. Or the character vector contains the unique prefix of sample names that are used for defining different sample groups. If missing all samples are assumed to be from one group
plot_type,	determins what type the plot will be, choose from "error_bar" or "hist". Only relevant when by_chr=TRUE

Value

ggplot object

Examples

demo_path <-paste0(system.file("extdata",package = "comapr"),"/")
s1_rse_state <- readHapState("s1",chroms=c("chr1"),
                             path=demo_path,barcodeFile=NULL,minSNP = 0,
                             minlogllRatio = 50,
                             bpDist = 100,maxRawCO=10,
                             minCellSNP = 0)
s1_count <- countCOs(s1_rse_state)
plotCount(s1_count)

ruqianl/comapr documentation built on Oct. 27, 2023, 5:12 a.m.