acgplot: Aggregated Cells Gene Plot

In pwirapati/acdx: Aggregated Cell Differential Expression

Description

Forest plot of the aggregated cells summaries for a given gene

Usage

acgplot( ac, gene, 
  o = NULL,
  sample_tags = NULL,
  fit=NULL,
  adjusted=FALSE,
  conf.bar=FALSE,
  s=.5,
  pch=20,
  col.dot=NULL,
  N.dot=TRUE,
  cex.dot=0.8,
  lwd.conf=1,
  lty.conf=1,
  las=c(0,0),
  legend.key=NULL,
  pbulk=F,
  ... )    # options to 'plot.default'

Arguments

ac	Aggregated cell data object produced by greg
gene	Name of the gene to be displayed
o	Ordering of the sample. Default to '1:n_sample'.
sample_tags	A data frame of sample tags to be displayed below the x-axis. The rows must match the samples in the ac object.
fit	A fitted model object from acdx. This allows displaying adjusted/normalized data.
adjusted	If fit= is defined, show adjusted counts instead of raw counts.
conf.bar	Show confidence bars. (Note: this is only approximate 95% confidence bars, not for inference purpose.)
s	A constant shift for the log-transformation for plotting. This is unrelated to any analysis, and only to allow the zero counts to be displayed on the plot, with y-axis still matching the original value before shifting.
pch	Dot type (default is filled circles)
col.dot	Colors for the dots. The colors can be made sample specific and has to be supplied in the same order as in the ac object. If o= is supplied, it will be used.
N.dot	Dot size is proportional to log number of cells
cex.dot	Dot size scale factor
lwd.conf	Line width of confidence bars.
lty.conf	Line type of confidence bars.
las	Group label directionality
legend.key	A vector of dot colors with names corresponding to the labels to be shown in the legend. Used in conjuction with col.dot=
pbulk	Show the sum (mean multiplied by the number of cells)
...	Other options to plot

Examples

  ## see the 'quick tutorial'

pwirapati/acdx documentation built on Jan. 11, 2021, 12:31 a.m.