autoplot.nacho: Plot quality-control metrics and thresholds of a "nacho"...

In NACHO: NanoString Quality Control Dashboard

Plot quality-control metrics and thresholds of a "nacho" object

Description

This function allows to plot any qualit-control figures available within the shiny app using visualise() or in the HTML report from render().

Usage

## S3 method for class 'nacho'
autoplot(
  object,
  x,
  colour = "CartridgeID",
  size = 0.5,
  show_legend = TRUE,
  show_outliers = TRUE,
  outliers_factor = 1,
  outliers_labels = NULL,
  ...
)

Arguments

object	[list] List obtained from load_rcc() or normalise().
x	[character] Character string naming the quality-control metrics to plot from nacho_object. The possible values are: "BD" (Binding Density) "FoV" (Imaging) "PCL" (Positive Control Linearity) "LoD" (Limit of Detection) "Positive" (Positive Controls) "Negative" (Negative Controls) "Housekeeping" (Housekeeping Genes) "PN" (Positive Controls vs. Negative Controls) "ACBD" (Average Counts vs. Binding Density) "ACMC" (Average Counts vs. Median Counts) "PCA12" (Principal Component 1 vs. 2) "PCAi" (Principal Component scree plot) "PCA" (Principal Components planes) "PFNF" (Positive Factor vs. Negative Factor) "HF" (Housekeeping Factor) "NORM" (Normalisation Factor)
colour	[character] Character string of the column in ssheet_csv or more generally in nacho_object$nacho to be used as grouping colour.
size	[numeric] A numeric controlling point size (ggplot2::geom_point() or line size (ggplot2::geom_line()).
show_legend	[logical] Boolean to indicate whether the plot legends should be plotted (TRUE) or not (FALSE). Default is TRUE.
show_outliers	[logical] Boolean to indicate whether the outliers should be highlighted in red (TRUE) or not (FALSE). Default is TRUE.
outliers_factor	[numeric] Size factor for outliers compared to size. Default is 1.
outliers_labels	[character] Character to indicate which column in nacho_object$nacho should be used to be printed as the labels for outliers or not. Default is NULL.
...	Other arguments (Not used).

Examples

data(GSE74821)

autoplot(GSE74821, x = "BD")

NACHO documentation built on Aug. 8, 2023, 1:08 a.m.