Plot multiple trends of the multiple genes.

Plot trends of multiple genes (clustered) across the binned pseudotime.

plotTrendCluster(
  scmpObj,
  xlab = "Pooled Pseudotime",
  ylab = "log(Pseudobulk Expression)",
  plot = "counts",
  summary_mode = "median",
  logs = TRUE,
  logType = "log",
  smoothness = 1,
  includeInflu = TRUE,
  verbose = TRUE,
  pseudoCount = 1,
  significant = FALSE,
  curves = TRUE,
  lines = FALSE,
  points = TRUE,
  parallel = FALSE,
  loess_span = 0.8
)

Arguments

scmpObj

An object of class ScMaSigPro.

xlab

X-axis label. (Default is "Pooled Pseudotime")

ylab

Y-axis label. (Default is "Pseudobulk Expression")

plot

Whether to plot 'coeff' or 'counts'. (Default is 'counts')

summary_mode

Compress the expression values per replicate (if present) per binned pseudotime point. Default is 'median'. Other option 'mean'

logs

Whether to log transform counts. (Default is TRUE)

logType

How to log transform the values. Available options 'log', 'log2', 'log10'. (Default is 'log')

smoothness

How smooth the trend should be. Setting to higher values will result in more linear trends. (Default is 0.01)

includeInflu

Include gene only if it has influential data. (Default is TRUE)

verbose

Print detailed output in the console. (Default is TRUE)

pseudoCount

Add a pseudo-count before taking the log. (Default is 1)

significant

Include gene only if the models are significant based on scMaSigPro::sc.filter(). (Default is TRUE)

curves

Whether to plot the fitted curves. (Default is TRUE)

lines

Whether to plot the lines. (Default is FALSE)

points

Whether to plot the points. (Default is TRUE)

parallel

Use forking process to run parallelly. (Default is FALSE) (Currently, Windows is not supported)

loess_span

The fraction of the data used when estimating each y-value, when plotting curves. (Default is 0.75)

Value

ggplot2 plot object.

Author

Priyansh Srivastava spriyansh29@gmail.com