plotInfReps: Plot inferential replicates for a gene or transcript

In mikelove/fishpond: Fishpond: downstream methods and tools for expression data

Plot inferential replicates for a gene or transcript

Description

For datasets with inferential replicates, boxplots are drawn for the two groups and potentially grouped by covariates. For datasets with only mean and variance, points and intervals (95 approximation) are drawn. Additionally, for numeric x values, points and intervals will be drawn and computeInfRV should be run first in order to add the mean and variance statistics.

Usage

plotInfReps(
  y,
  idx,
  x,
  cov = NULL,
  colsDrk = c("dodgerblue", "goldenrod4", "royalblue4", "red3", "purple4", "darkgreen"),
  colsLgt = c("lightblue1", "goldenrod1", "royalblue1", "salmon1", "orchid1",
    "limegreen"),
  xaxis,
  xlab,
  ylim,
  main,
  mainCol,
  legend = FALSE,
  legendPos = "topleft",
  legendTitle = FALSE,
  legendCex = 1,
  useMean = TRUE,
  q = qnorm(0.975),
  applySF = FALSE,
  reorder,
  thin,
  shiftX
)

Arguments

y	a SummarizedExperiment (see swish)
idx	the name or row number of the gene or transcript
x	the name of the condition variable for splitting and coloring the samples or cells. Also can be a numeric, e.g. pseudotime, in which case, cov can be used to designate groups for coloring
cov	the name of the covariate for adjustment
colsDrk	dark colors for the lines of the boxes
colsLgt	light colors for the inside of the boxes
xaxis	logical, whether to label the sample numbers. default is TRUE if there are less than 30 samples
xlab	the x-axis label
ylim	y limits
main	title
mainCol	name of metadata column to use for title (instead of rowname)
legend	logical, show simple legend (default FALSE)
legendPos	character, position of the legend (default "topleft")
legendTitle	logical, whether to add the name of the grouping variable as a title on the legend (default FALSE)
legendCex	numeric, size of the legend (default 1)
useMean	logical, when inferential replicates are not present or when x is continuous, whether to use the mean assay or the counts assay for plotting
q	numeric, the quantile to use when plotting the intervals when inferential replicates are not present or when x is continuous. Default is qnorm(.975) ~= 1.96 corresponding to 95 intervals
applySF	logical, when inferential replicates are not present, should y$sizeFactor be divided out from the mean and interval plots (default FALSE)
reorder	logical, should points within a group defined by condition and covariate be re-ordered by their count value (default is FALSE, except for alevin data)
thin	integer, should the mean and interval lines be drawn thin (the default switches from 0 [not thin] to 1 [thinner] at n=150 cells, and from 1 [thinner] to 2 [thinnest] at n=400 cells)
shiftX	when x is continuous and cov is provided, the amount to shift the values on the x-axis to improve visibility of the point and line ranges (will be subtracted from the first level of cov and added to the second level of cov)

Value

nothing, a plot is displayed

Examples

y <- makeSimSwishData()
plotInfReps(y, 3, "condition")

y <- makeSimSwishData(n=40)
y$batch <- factor(rep(c(1,2,3,1,2,3),c(5,10,5,5,10,5)))
plotInfReps(y, 3, "condition", "batch")

mikelove/fishpond documentation built on Aug. 29, 2023, 2:45 p.m.