plot_scatter: Plotting the results.

In angelesarzalluz/scfilters: A correlation-based method for quality filtering of single-cell RNAseq data

Description

This set of functions generate the summary plots that result from the correlation-based analysis of your single-cell sequencing data.

Usage

plot_scatter(data, save = FALSE, display = TRUE, path = ".",
  filename = "scatter_plot", format = "png", density = FALSE,
  shape = 16, size = 0.5, alpha = 0.5, ...)

plot_bins(data, save = FALSE, display = TRUE, path = ".",
  filename = "bins_plot", format = "png", shape = 16, alpha = 0.5,
  size = 0.5, ...)

plot_cor_dens(data, save = FALSE, display = TRUE, path = ".",
  filename = NULL, format = "png", window, ribbon_col = "grey",
  ribbon_alpha = 0.2, ..., curve_cols = c("black", "red"))

plot_histogram(data, save = FALSE, display = TRUE, path = ".",
  filename = "histogram", format = "png", title, ylim = 1, ...)

Arguments

data	A data frame containing the suitably formatted data for the specified plot.
save	A logical. When TRUE, plots will be saved to the indicated path.
display	A logical. When TRUE, plots will be displayed.
path	A string indicating a path to save the plot to.
filename	A string indicating the name of the plot file.
format	A string indicating the file format of the plot.
density	Logical. Specifies whether the scatter plot will incorporate scatter density lines.
shape,	size, alpha Numbers specifying aesthetics of the scatter plots, passed on to the geom_point function in the ggplot2 package. Shape is an integer, size and alpha are doubles.
...	Other aesthetic specifications to be passed on to the geom_point, geom_line or geom_bar functions.
window	An integer. Indicates the window for which the correlation density plot is being generated by plot_cor_dens.
ribbon_col,	ribbon_alpha Aesthetics for the error space in the correlation density plot. Color indicated by a string, and alpha indicated by a double.
curve_cols	A string vector. Specifies colours of the negative control and data curves in the correlation density plots, in that order.
title	A string. Contains the title to be set on the histogram plot, normally an informative title. Recommendation is to specify top window method of selection and size, number and size of bins, number of cells in the original dataset.
ylim	A double. Sets the limit of the y axis.

Details

Each plotting function is designed to plot the output data of another function in this package. Associations are as follows:

• plot_scatter plots the output of the calculate_cvs function, more specifically, only the CV and mean columns. However, the plotting function selects these automatically, and the entire data frame should be provided by the user when calling it.

  If running all_calls, this can be done by subsetting the results using $cv.

• plot_bins plots the output of the bin_scdata function. Similarly, the entire data frame should be provided, as the function will select the CV, mean and bin columns automatically from it.

  Subset the appropriate results from all_calls using $binned.

• plot_cor_dens plots the output of the compute_density function.It should be noted that this function outputs the density computations for only one window, and therefore, the plotting function must be called again after each computation.

  Subset the appropriate results from all_calls using $densities[[window number]].

• plot_histogram plots the output of the compute_histogram function. Subset all_calls results using $histogram.

For the ... argument:

• plot_scatter and plot_bins pass on the arguments to the geom_point function in ggplot2.

• plot_cor_dens passes arguments on to the geom_line function in ggplot2.

• plot_histogram passes arguments on to geom_bar function in ggplot2.

For suitable aesthetics, please see documentation of these functions.

Important note: calling the plotting functions doesn't enable visualization of the plot. The plot list that is generated should be saved and then visualized by calling the plot function on it.

Value

A list, containing the information of the generated plot.

angelesarzalluz/scfilters documentation built on May 10, 2019, 11:46 a.m.