NanoStringRccSet-autoplot: Plot NanoStringRccSet Data

In Nanostring-Biostats/NanoStringNCTools: NanoString nCounter Tools

Plot NanoStringRccSet Data

Description

Generate common plots to visualize and QC NanoStringRccSet data.

Usage

       ## S3 method for class 'NanoStringRccSet'
autoplot(object,
           type = c("boxplot-feature",
                    "boxplot-signature",
                    "bindingDensity-mean",
                    "bindingDensity-sd",
                    "ercc-linearity",
                    "ercc-lod",
                    "heatmap-genes",
                    "heatmap-signatures",
                    "housekeep-geom",
                    "lane-bindingDensity",
                    "lane-fov",
                    "mean-sd-features",
                    "mean-sd-samples"),
           log2scale = TRUE,
           elt = "exprs",
           index = 1L,
           geomParams = list(),
           tooltipDigits = 4L,
           heatmapGroup = NULL,
           blacklist = NULL,
           tooltipID = NULL,
           qcCutoffs = list(
             Housekeeper = c("failingCutoff" = 32,"passingCutoff" = 100) ,
             Imaging = c("fovCutoff" = 0.75) ,
             BindingDensity = c("minimumBD" = 0.1, "maximumBD" = 2.25, 
                                "maximumBDSprint" = 1.8) ,
             ERCCLinearity = c("correlationValue" = 0.95) ,
             ERCCLoD = c("standardDeviations" = 2) ),
           scalingFactor=1L,
           show_rownames_gene_limit=60L,
           show_colnames_gene_limit=36L,
           show_rownames_sig_limit=60L,
           show_colnames_sig_limit=36L,
           subSet = NULL ,
           ...)

Arguments

object	A NanoStringRccSet object
type	Character string referencing the type of plot to generate
log2scale	An optional boolean indicating expression data is on log2 scale
elt	An optional character string of the expression matrix name
index	An optional integer giving the feature of interest row location
geomParams	An option list of parameters for geometry
tooltipDigits	An optional integer for number of tooltip decimal places to display
heatmapGroup	An optional character string referencing pData column to color samples by in heatmap
blacklist	An optional character vector of features not to plot
tooltipID	An optional character string referencing pData column to use for sample ID in the tooltip
qcCutoffs	An optional list of QC cutoffs
scalingFactor	An optional numeric value indicating a scaling factor to apply to plot drawing
show_rownames_gene_limit	An optional integer limit on number of features to display row-wise
show_colnames_gene_limit	An optional integer limit on number of features to display column-wise
show_rownames_sig_limit	An optional integer limit on number of signatures to display row-wise
show_colnames_sig_limit	An optional integer limit on number of signatures to display column-wise
subSet	An optional subset to plot on
...	Additional arguments to pass on to autoplot function

Details

"boxplot-feature"

Generate feature boxplots

"boxplot-signature"

Generate signature boxplots

"bindingDensity-mean"

Plot binding density displayed as average expression

"bindingDensity-sd"

Plot binding density displayed as standard deviation of expression

"ercc-linearity"

Assess linearity of ERCCs

"ercc-lod"

Assess limit of detection based on ERCC expression

"heatmap-genes"

Generate a heatmap from feature expression

"heatmap-signatures"

Generate a heatmap from signature expression

"housekeep-geom"

Plot geometric mean of housekeeper genes

"lane-bindingDensity"

View binding density by lane

"lane-fov"

Assess image quality by lane

"mean-sd-features"

Plot mean versus standard deviation feature-wise

"mean-sd-samples"

Plot mean versus standard deviation sample-wise

Value

A ggplot or pheatmap plot depending on the type of plot generated

Examples

# Create NanoStringRccSet from data files
datadir <- system.file("extdata", "3D_Bio_Example_Data",
                       package = "NanoStringNCTools")
rccs <- dir(datadir, pattern = "SKMEL.*\\.RCC$", full.names = TRUE)
rlf <- file.path(datadir, "3D_SolidTumor_Sig.rlf")
pheno <- file.path(datadir, "3D_SolidTumor_PhenoData.csv")
solidTumor <-
  readNanoStringRccSet(rccs, rlfFile = rlf, phenoDataFile = pheno)

# Assess experiment linearity
#autoplot(solidTumor, "ercc-linearity")

# Plot a feature's expression across all samples
#autoplot(solidTumor, "boxplot-feature", index=2)

Nanostring-Biostats/NanoStringNCTools documentation built on Dec. 18, 2024, 1:24 a.m.