plotROIQC: Plot Sample-wise QC plot

In DavisLaboratory/standR: Spatial transcriptome analyses of Nanostring's DSP data in R

Plot Sample-wise QC plot

Description

Plot Sample-wise QC plot

Usage

plotROIQC(
  spe_object,
  x_axis = "AOINucleiCount",
  y_axis = "lib_size",
  x_lab = "AOINucleiCount",
  y_lab = "Library size",
  x_threshold = NULL,
  y_threshold = NULL,
  regression_col = "purple",
  hist_col = "black",
  hist_fill = "white",
  bin_num = 50,
  threshold_col = "red",
  threshold_linetype = "dashed",
  layout_ncol = 2,
  layout_nrow = 2,
  leyout_height = c(0.8, 2.5),
  layout_width = c(2.5, 0.8),
  ...
)

Arguments

spe_object	A SpatialExperiment object.
x_axis	Numeric feature to plot as x axis.
y_axis	Numeric feature to plot as y axis.
x_lab	Label name for x axis.
y_lab	Label name for y axis.
x_threshold	Threshold to draw.
y_threshold	Threshold to draw.
regression_col	Color for the regression line.
hist_col	Color for the histograms.
hist_fill	Fill for the histograms.
bin_num	Bin numbers for the histograms.
threshold_col	Threshold line color.
threshold_linetype	Threshold line type.
layout_ncol	Column number layout.
layout_nrow	Row number layout.
leyout_height	Height layout.
layout_width	Width layout.
...	aesthetic mappings to pass to ggplot2::aes() of the dot plots.

Value

A ggplot object.

Examples

library(ggplot2)
library(patchwork)
data("dkd_spe_subset")
spe <- addPerROIQC(dkd_spe_subset)

plotROIQC(spe)

DavisLaboratory/standR documentation built on March 28, 2024, 4:23 a.m.