plotMetric: Plot metrics present in a 'CNVMetric' object
In adeschen/CNVMetrics: Copy Number Variant Metrics

plotMetric

R Documentation

Plot metrics present in a `CNVMetric` object

Description

This function plots one heatmap (or two heatmaps) of the metrics present in a CNVMetric object. For the overlapping metrics, the user can select to print the heatmap related to amplified or deleted regions or both. The NA values present in the metric matrix are transformed into zero for the creation of the heatmap.

Usage

plotMetric(
  metric,
  type = "ALL",
  colorRange = c(c("white", "darkblue")),
  show_colnames = FALSE,
  silent = TRUE,
  ...
)

Arguments

`metric`	a `CNVMetric` object containing the metrics calculated by `calculateOverlapMetric` or by `calculateLog2ratioMetric`.
`type`	a single `character` string indicating which graph to generate. This should be a type present in the `CNVMetric` object or "`ALL`". This is useful for the overlapping metrics that have multiple types specified by the user. Default: "`ALL`".
`colorRange`	a `vector` of 2 `character` string representing the 2 colors that will be assigned to the lowest (0) and highest value (1) in the heatmap. Default: `c("white", "darkblue")`.
`show_colnames`	a `boolean` specifying if column names are be shown. Default: `FALSE`.
`silent`	a `boolean` specifying if the plot should not be drawn. Default: `TRUE`.
`...`	further arguments passed to `pheatmap::pheatmap()` method. Beware that the `filename` argument cannot be used when `type` is "`ALL`".

Value

a gtable object containing the heatmap(s) of the specified metric(s).

Author(s)

Astrid Deschênes

Examples


## Load required package to generate the samples
require(GenomicRanges)

## Create a GRangesList object with 3 samples
## The stand of the regions doesn't affect the calculation of the metric
demo <- GRangesList()
demo[["sample01"]] <- GRanges(seqnames="chr1",
    ranges=IRanges(start=c(1905048, 4554832, 31686841),
    end=c(2004603, 4577608, 31695808)), strand="*",
    state=c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))

demo[["sample02"]] <- GRanges(seqnames="chr1",
    ranges=IRanges(start=c(1995066, 31611222, 31690000),
    end=c(2204505, 31689898, 31895666)), strand=c("-", "+", "+"),
    state=c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))

## The amplified region in sample03 is a subset of the amplified regions
## in sample01
demo[["sample03"]] <- GRanges(seqnames="chr1",
    ranges=IRanges(start=c(1906069, 4558838),
    end=c(1909505, 4570601)), strand="*",
    state=c("AMPLIFICATION", "DELETION"))

## Calculating Sorensen metric
metric <- calculateOverlapMetric(demo, method="sorensen")

## Plot both amplification and deletion metrics
plotMetric(metric, type="ALL")

## Extra parameters, used by pheatmap(), can also be passed to the function
## Here, we have the metric values print to the cell while the
## row names and column names are removed
plotMetric(metric, type="DELETION", show_rownames=FALSE,
    show_colnames=FALSE, main="deletion", display_numbers=TRUE,
    number_format="%.2f")

adeschen/CNVMetrics documentation built on July 19, 2023, 10:24 p.m.