plotGeneQC: Plot gene-wise QC plot

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

Plot gene-wise QC plot

Description

Plot gene-wise QC plot

Usage

plotGeneQC(
  spe,
  top_n = 9,
  ordannots = c(),
  point_size = 1,
  line_type = "dashed",
  line_col = "darkred",
  line_cex = 1,
  hist_col = "black",
  hist_fill = "skyblue",
  bin_num = 30,
  text_size = 13,
  layout_ncol = 1,
  layout_nrow = 2,
  layout_height = c(1, 1),
  ...
)

Arguments

spe	A SpatialExperiment object.
top_n	Integer. Indicating the top n genes will be plotted. Default is 9.
ordannots	variables or computations to sort samples by (tidy style).
point_size	Numeric. Point size.
line_type	Character. Line types for ggplot.
line_col	Color for line.
line_cex	Cex for line.
hist_col	Color for histogram.
hist_fill	Fill for histogram.
bin_num	Bin numbers for histogram.
text_size	Text size.
layout_ncol	Integer. Column number for layout. Default is 1.
layout_nrow	Integer. Row number for layout. Default is 2.
layout_height	Vector of numerics with length of 2. Default is c(1, .4).
...	aesthetic mappings to pass to ggplot2::aes() of the dot plots.

Value

A ggplot object

Examples

data("dkd_spe_subset")
spe <- addPerROIQC(dkd_spe_subset)
plotGeneQC(spe)

DavisLaboratory/standR documentation built on Sept. 8, 2024, 9:57 p.m.