plotDeaVolcano: Plot DEA results via volcano plots
In theMILOlab/SPATA2: A Toolbox for Spatial Expression Analysis

plotDeaVolcano

R Documentation

Plot DEA results via volcano plots

Description

Plots a common volcano plot with p-value on the y- and logfold change on the x-axis.

Usage

plotDeaVolcano(
  object,
  across = getDefaultGrouping(object),
  across_subset = NULL,
  relevel = TRUE,
  method_de = NULL,
  color_up = "tomato",
  color_down = "steelblue",
  color_insignif = "lightgrey",
  pt_alpha = 0.9,
  pt_size = 1,
  threshold_logFC = 1,
  threshold_pval = 0.01,
  label_genes = 5,
  label_insignificant = TRUE,
  label_side = c("up", "down"),
  label_size = 1,
  nrow = NULL,
  ncol = NULL,
  scales = "fixed",
  use_pseudolog = FALSE,
  assay_name = activeAssay(object),
  ...
)

plotDeaVolcano1v1(
  object,
  across,
  method_de = NULL,
  clrp = NULL,
  clrp_adjust = NULL,
  color_insignif = "lightgrey",
  pt_alpha = 0.9,
  pt_size = 1,
  threshold_logFC = 1,
  threshold_pval = 0.01,
  col_pval = "p_val_adj",
  label_genes = 5,
  label_size = 1,
  use_pseudolog = FALSE,
  limits = NULL,
  display_title = TRUE,
  title_size = 2,
  digits = 2,
  assay_name = activeAssay(object),
  ...
)

Arguments

`object`	An object of class `SPATA2` or, in case of S4 generics, objects of classes for which a method has been defined.
`across`	Character value or NULL. Specifies the grouping variable of interest. Use `getGroupingOptions()` to obtain all variable names that group the barcode spots of your object in a certain manner.
`across_subset`	Character vector or NULL. Specifies the particular groups of interest the grouping variable specified in argument `across` contains. If set to NULL all of them are chosen. You can prefix groups you are NOT interested in with a '-'. (Saves writing if there are more groups you are interested in than groups you are not interested in.) Use `getGroupNames()` to obtain all valid input options.
`relevel`	Logical value. If set to TRUE the input order of `across_subset` determines the order in which the groups of interest are displayed. Groups that are not included are dropped which affects the colors with which they are displayed.
`method_de`	Character value. Denotes the method to according to which the de-analysis is performed. Given to argument `test.use` of the `Seurat::FindAllMarkers()`-function. Run `SPATA::dea_methods` to obtain all valid input options.
`color_up`	Character value. Color of points that represent upregulated genes.
`color_down`	Character value. Color of poitns that represent downregulated genes.
`color_insignif`	Character value. Color of points that fall below the threshold set via argument `threshold_pval`.
`pt_alpha`	Numeric value. Specifies the degree of transparency of all points.
`pt_size`	Numeric value. Specifies the size of all points.
`threshold_logFC`	Numeric value. Denotes the threshold for the logFC. Genes with a logFC below are displayed as not significant.
`threshold_pval`	Numeric value. Denotes the threshold for the p-value. Genes with a p-value above are displayed as not significant.
`label_genes`	Specify which genes are labeled in the plot. If numeric, specifies the number of genes that are labeled. E.g. if `label_genes` = 5, the default, the top 5 genes are labeled. If character, specifies the genes that are supposed to be labeled by name. If `NULL` or `FALSE`, no genes are labeled.
`label_insignificant`	Logical value. If `FALSE`, insignifcant genes are not labeled.
`label_side`	Character vector. Decides on which side to label genes. Valid input are 'up' and/or 'down'.
`nrow`, `ncol`	Numeric values or NULL. Used to arrange multiple plots.
`use_pseudolog`	Logical value. If TRUE, avglogFC is transformed with log10. Requires package `ggallin` to be installed.
`assay_name`	Only relevant if the `SPATA2` object contains more than one assay: Denotes the assay of interest and thus the molecular modality to use. Defaults to the active assay as set by `activateAssay()`.
`...`	Used to absorb deprecated arguments or functions.
`clrp`	Character value. Specifies the color palette to be used to represent groups of discrete variables. Run `validColorPalettes()` to obtain valid input options.
`clrp_adjust`	Named character vector or NULL. If character, it adjusts the color palette that is used to represent the groups. Names of the input vector must refer to the group and the respective named element denotes the color with which to represent the group.
`display_title`	Logical value. If set to TRUE an informative title is displayed.