Plot trend of the single gene.

Plot trend of the single gene across the binned pseudotime.

plotTrend(
  scmpObj,
  feature_id,
  xlab = "Pooled Pseudotime",
  ylab = "Pseudobulk Expression",
  smoothness = 0.01,
  logs = TRUE,
  logType = "log",
  pseudoCount = 1,
  significant = TRUE,
  summary_mode = "median",
  curves = TRUE,
  lines = FALSE,
  points = TRUE
)

Arguments

scmpObj

An object of class ScMaSigPro.

feature_id

Name of the gene to be plotted.

xlab

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

ylab

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

smoothness

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

logs

Whether to log transform counts. (Default is TRUE)

logType

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

pseudoCount

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

significant

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

summary_mode

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

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)

Value

ggplot2 plot object.

Author

Priyansh Srivastava spriyansh29@gmail.com