plotDimReduceModule: Plotting the Celda module probability on a dimensionality...

Description Usage Arguments Value Examples

View source: R/plot_dr.R

Description

Create a scatterplot for each row of a normalized gene expression matrix where x and y axis are from a data dimensionality reduction tool. The cells are colored by the module probability(s).

Usage

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plotDimReduceModule(
  dim1,
  dim2,
  counts,
  celdaMod,
  modules = NULL,
  rescale = TRUE,
  size = 1,
  xlab = "Dimension_1",
  ylab = "Dimension_2",
  colorLow = "grey",
  colorMid = NULL,
  colorHigh = "blue",
  ncol = NULL
)

Arguments

dim1

Numeric vector. First dimension from data dimensionality reduction output.

dim2

Numeric vector. Second dimension from data dimensionality reduction output.

counts

Integer matrix. Rows represent features and columns represent cells. This matrix should be the same as the one used to generate 'celdaMod'.

celdaMod

Celda object of class "celda_G" or "celda_CG".

modules

Character vector. Module(s) from celda model to be plotted. e.g. c("1", "2").

rescale

Logical. Whether rows of the matrix should be rescaled to [0, 1]. Default TRUE.

size

Numeric. Sets size of point on plot. Default 1.

xlab

Character vector. Label for the x-axis. Default "Dimension_1".

ylab

Character vector. Label for the y-axis. Default "Dimension_2".

colorLow

Character. A color available from 'colors()'. The color will be used to signify the lowest values on the scale. Default 'grey'.

colorMid

Character. A color available from 'colors()'. The color will be used to signify the midpoint on the scale.

colorHigh

Character. A color available from 'colors()'. The color will be used to signify the highest values on the scale. Default 'blue'.

ncol

Integer. Passed to facet_wrap. Specify the number of columns for facet wrap.

Value

The plot as a ggplot object

Examples

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data(celdaCGSim, celdaCGMod)
celdaTsne <- celdaTsne(
  counts = celdaCGSim$counts,
  celdaMod = celdaCGMod
)
plotDimReduceModule(
  dim1 = celdaTsne[, 1], dim2 = celdaTsne[, 2],
  counts = celdaCGSim$counts, celdaMod = celdaCGMod,
  modules = c("1", "2")
)

celda documentation built on June 9, 2020, 2 a.m.