WaterfallPlot: Waterfall Plot

In huayc09/SeuratExtend: SeuratExtend

Waterfall Plot

Description

Generates a waterfall plot.

Usage

WaterfallPlot(object, ...)

## S3 method for class 'Seurat'
WaterfallPlot(
  seu,
  features,
  group.by = NULL,
  cell = NULL,
  slot = "data",
  assay = NULL,
  priority = c("expr", "none"),
  ident.1 = NULL,
  ident.2 = NULL,
  exp.transform = (length == "logFC"),
  order = TRUE,
  length = "logFC",
  color = "p",
  len.threshold = 0,
  col.threshold = 0,
  color_theme = c(low = muted("blue"), mid = "white", high = muted("red")),
  top.n = NULL,
  flip = FALSE,
  y.label = length,
  angle = NULL,
  hjust = NULL,
  vjust = NULL,
  title = NULL
)

## Default S3 method:
WaterfallPlot(
  matr,
  f,
  ident.1 = NULL,
  ident.2 = NULL,
  exp.transform = FALSE,
  order = TRUE,
  length = "tscore",
  color = "tscore",
  len.threshold = 0,
  col.threshold = 0,
  color_theme = c(low = muted("blue"), mid = "white", high = muted("red")),
  top.n = NULL,
  flip = TRUE,
  y.label = NULL,
  angle = NULL,
  hjust = NULL,
  vjust = NULL,
  title = NULL
)

Arguments

object	Either a Seurat object or a matrix.
...	Additional arguments passed to other methods.
seu	A Seurat object. Only applicable when using the Seurat method.
features	Features to be plotted, which can include gene expression, metrics, PC scores, or any other data that can be retrieved using the 'FetchData()' function. Only applicable for the Seurat method.
group.by	A variable from 'meta.data' for grouping, or a character vector of the same length as the number of cells. Only applicable for the Seurat method.
cell	Cell identifiers to be used in the plot. Defaults to all cells. Only applicable for the Seurat method.
slot	Slot from which to retrieve feature data. Only applicable for the Seurat method.
assay	Name of the assay to use. If not specified, the active assay will be used. Only applicable for the Seurat method.
priority	If set to "expr", the function will fetch data from the expression matrix rather than 'meta.data'. Only applicable for the Seurat method.
ident.1	The primary identity class. If not specified, the first class will be used.
ident.2	An optional secondary identity class for comparison. If NULL, comparisons will be made against all other cells.
exp.transform	Indicates whether to transform data using 'expm1'. This is particularly useful when calculating the log fold change of normalized gene counts. Defaults to FALSE for matrix input and TRUE for Seurat object input.
order	Determines whether the features should be ordered. Defaults to TRUE.
length	Specifies the statistic to determine the length of the bar. Possible values are "tscore" (default for matrix input), "p", or "logFC" (default for Seurat object input).
color	Specifies the statistic to determine the color of the bar. Possible values are "tscore" (default), "p" (default for Seurat object input), or "logFC".
len.threshold	Excludes features with a value for the 'length' parameter below this threshold. Defaults to 0.
col.threshold	Excludes features with a value for the 'color' parameter below this threshold. Defaults to 0.
top.n	Retains only the top 'n' bars in both positive and negative directions. If 'length(top.n)' is 1, the function retains 'top.n' bars for both positive and negative directions. If 'length(top.n)' is 2, it retains 'top.n[1]' positive bars and 'top.n[2]' negative bars. Defaults to NULL.
flip	Determines whether the plot should be flipped. Defaults to TRUE for matrix input and FALSE for Seurat object input.
y.label	Label for the y-axis. Defaults to "length".
angle	Angle of the x-axis labels. This argument is passed to 'element_text()'.
hjust	Horizontal justification for the x-axis labels. This argument is passed to 'element_text()'.
vjust	Vertical justification for the x-axis labels. This argument is passed to 'element_text()'.
title	Title of the plot. Defaults to NULL.
matr	A matrix or data frame where rows represent features and columns represent cells.
f	A factor or vector indicating the identity of each cell. The length should match the number of columns in 'matr'.
color_scheme	Specifies the color gradient for the heatmap visualization. This parameter accepts multiple input formats to provide flexibility in defining color schemes: - Predefined color schemes: Users can specify "A", "B", "C", "D", or "E" to use color schemes from the 'viridis' package. - Named vector for three-point gradients: Provide a named vector with keys "low", "mid", and "high" to define colors at these specific data points. The "mid" value is typically centered at zero, allowing for a diverging color scheme. Example: 'c(low = "blue", mid = "white", high = "red")' - Two-point gradient: Provide a named vector with keys "low" and "high" to create a simple two-color gradient. Example: 'c(low = "blue", high = "red")' - Custom color gradient: Users can provide a vector of colors to generate a custom gradient across multiple values. This is suitable for more complex data ranges and visual preferences.

Details

For more detailed usage, see the examples provided.

Value

A ggplot object.

Examples

# First, create a matrix using the GeneSetAnalysis() function.
# Rows represent the Hallmark 50 genesets, and columns represent cells.
pbmc <- GeneSetAnalysis(pbmc, genesets = hall50$human)
matr <- pbmc@misc$AUCell$genesets

# Generate a waterfall plot comparing CD14+ Mono with CD8 T cells.
WaterfallPlot(matr, f = pbmc$cluster, ident.1 = "Mono CD14", ident.2 = "CD8 T cell")

# Keep only bars with a length (tscore, in this instance) greater than 1.
WaterfallPlot(matr, f = pbmc$cluster, ident.1 = "Mono CD14", ident.2 = "CD8 T cell", len.threshold = 1)

# Use a Seurat object as input and compare 100 genes, using LogFC as bar length.
genes <- VariableFeatures(pbmc)[1:80]
WaterfallPlot(
  pbmc, group.by = "cluster", features = genes,
  ident.1 = "Mono CD14", ident.2 = "CD8 T cell", length = "logFC")

# Keep only the top and bottom 20 genes.
WaterfallPlot(
  pbmc, group.by = "cluster", features = genes,
  ident.1 = "Mono CD14", ident.2 = "CD8 T cell", length = "logFC",
  top.n = 20)

huayc09/SeuratExtend documentation built on July 15, 2024, 6:22 p.m.