volcano_plot {fastTopics}

Volcano Plots for Visualizing Results of Differential Expression Analysis

Description

Create a “volcano” plot to visualize the results of a differential count analysis using a topic model. Here, the volcano plot is a scatterplot in which the posterior mean log-fold change (LFC), estimated by running the methods implemented in de_analysis, is plotted against the estimated z-score. Variations on this volcano plot may also be created, for example by showing f0 (the null-model estimates) instead of the z-scores. Use volcano_plotly to create an interactive volcano plot.

Usage

volcano_plot(
  de,
  k,
  labels,
  y = c("z", "f0"),
  do.label = volcano_plot_do_label_default,
  ymin = 1e-06,
  ymax = Inf,
  max.overlaps = Inf,
  plot.title = paste("topic", k),
  ggplot_call = volcano_plot_ggplot_call
)

## S3 method for class 'topic_model_de_analysis'
plot(x, ...)

volcano_plotly(
  de,
  k,
  file,
  labels,
  y = c("z", "f0"),
  ymin = 1e-06,
  ymax = Inf,
  width = 500,
  height = 500,
  plot.title = paste("topic", k),
  plot_ly_call = volcano_plot_ly_call
)

volcano_plot_do_label_default(lfc, y)

volcano_plot_ggplot_call(dat, y, plot.title, max.overlaps = Inf, font.size = 9)

volcano_plot_ly_call(dat, y, plot.title, width, height)

Arguments

de

An object of class “topic_model_de_analysis”, usually an output from de_analysis. It is better to run de_analysis with shrink.method = "ash" so that the points in the volcano plot can be coloured by their local false sign rate (lfsr).

k

The topic, selected by number or name.

labels

Character vector specifying how the points in the volcano plot are labeled. This should be a character vector with one entry per LFC estimate (row of de$postmean). When not specified, the row names of de$postmean are used. When available. labels are added to the plot using geom_text_repel.

y

A vector of the same length as lfc.

do.label

The function used to deetermine which LFC estimates to label. Replace volcano_plot_do_label_default with your own function to customize the labeling of points in the volcano plot.

ymin

Y-axis values less than ymin are shown as ymin.

ymax

Y-axis values greater than ymax are shown as ymax. When y = "z", setting ymax to a finite value can improve the volcano plot when some z-scores are much larger (in magnitude) than others.

max.overlaps

Argument passed to geom_text_repel.

plot.title

The title of the plot.

ggplot_call

The function used to create the plot. Replace volcano_plot_ggplot_call with your own function to customize the appearance of the plot.

x

An object of class “topic_model_de_analysis”, usually an output from de_analysis.

...

Additional arguments passed to volcano_plot.

file

Save the interactive volcano plot to this HTML file using saveWidget.

width

Width of the plot in pixels. Passed as argument “width” to plot_ly.

height

Height of the plot in pixels. Passed as argument “height” to plot_ly.

plot_ly_call

The function used to create the plot. Replace volcano_plot_ly_call with your own function to customize the appearance of the interactive plot.

lfc

A vector of log-fold change estimates.

dat

A data frame passed as input to ggplot, containing, at a minimum, columns “f0”, “postmean”, “y”, “lfsr” and “label”.

font.size

Font size used in plot.

Details

Interactive volcano plots can be created using the ‘plotly’ package. The “hover text” shows the label and detailed LFC statistics.

Value

A ggplot object or a plotly object.

See Also

de_analysis

Examples

# See help(de_analysis) for examples.