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DEtest Manhattan Plot

Source: R/DEtestPlot.R
DEtestManhattanPlot.Rd

Draw a Manhattan-style plot of differential expression results by cell type.

Usage

DEtestManhattanPlot(
  srt,
  group.by = NULL,
  test.use = "wilcox",
  res = NULL,
  group_use = NULL,
  DE_threshold = "avg_log2FC > 0 & p_val_adj < 0.05",
  group_palette = "Chinese",
  group_palcolor = NULL,
  pt.size = 1,
  pt.alpha = 1,
  cols.highlight = "black",
  sizes.highlight = 1,
  alpha.highlight = 1,
  stroke.highlight = 0.5,
  nlabel = 5,
  features_label = NULL,
  only.pos = FALSE,
  label.by = c("p_val_adj", "p_val", "diff_pct", "avg_log2FC"),
  label.fg = "black",
  label.bg = "white",
  label.bg.r = 0.1,
  label.size = 4,
  palette = "RdBu",
  palcolor = NULL,
  theme_use = "theme_scop",
  theme_args = list(),
  manhattan.bg = "white",
  group_track_width = NULL,
  group_track_height = NULL,
  jitter_width = 0.5,
  jitter_height = 0,
  seed = 11,
  aspect.ratio = NULL,
  xlab = NULL,
  ylab = NULL,
  verbose = TRUE
)

Arguments

srt

A Seurat object or SummarizedExperiment object containing the results of differential expression analysis.

group.by

Name of one or more meta.data columns to group (color) cells by.

test.use

A character string specifying the type of statistical test to use. Default is "wilcox".

res

A data.frame or data.table with differential expression results. When res is provided, srt will be ignored. The data.frame must contain columns: gene, group1 (factor or character), avg_log2FC, p_val_adj, and optionally pct.1 and pct.2 for calculating diff_pct.

group_use

Groups to plot. Default is NULL (all groups).

DE_threshold

A character string specifying the threshold for differential expression (used to highlight significant genes in all plot types). Default is "p_val < 0.05" for sample-level methods ("edgeR" and "limma") and "avg_log2FC > 0 & p_val_adj < 0.05" otherwise.

group_palette

Palette for cell types (groups) in Manhattan plot. Default is "Chinese".

group_palcolor

Custom colors for cell types (groups) in Manhattan plot. Default is NULL.

pt.size

The size of the points. Default is 1.

pt.alpha

The transparency of the data points. Default is 1.

cols.highlight

A character string specifying the color for highlighted points. Default is "black".

sizes.highlight

The size of the highlighted points. Default is 1.

alpha.highlight

The transparency of the highlighted points. Default is 1.

stroke.highlight

The stroke width for the highlighted points. Default is 0.5.

nlabel

An integer value specifying the number of labeled points per group. Default is 5.

features_label

A character vector specifying the feature labels to plot. Default is NULL.

only.pos

Whether to show only positive log2 fold-change results in differential expression visualizations. Default is FALSE.

label.by

Metric used to select automatic labels when features_label = NULL. Options are "p_val_adj", "p_val", "diff_pct", and "avg_log2FC". Smaller p-values are ranked first; diff_pct and avg_log2FC use the strongest positive and negative effects within each group. Default is "p_val_adj".

label.fg

A character string specifying the color for the labels' foreground. Default is "black".

label.bg

A character string specifying the color for the labels' background. Default is "white".

label.bg.r

The radius of the rounding of the labels' background. Default is 0.1.

label.size

The size of the labels. Default is 4.

palette

Color palette name. Available palettes can be found in thisplot::show_palettes. Default is "RdBu".

palcolor

Custom colors used to create a color palette. Default is NULL.

theme_use

Theme to use for the plot. Default is "theme_scop".

theme_args

A list of additional arguments to pass to the theme function. Default is list().

manhattan.bg

Background color for Manhattan plot. Default is "white".

group_track_width

Width of the centered cell-type track in Manhattan plot. Default is NULL, which uses the current automatic width.

group_track_height

Height of the centered cell-type track in Manhattan plot. Default is NULL, which uses the current automatic height.

jitter_width

Horizontal jitter range for points in Manhattan plot. Default is 0.5.

jitter_height

Vertical jitter range for points in Manhattan plot. Default is 0.

seed

Random seed for jitter in Manhattan and ring plots. Default is 11.

aspect.ratio

Aspect ratio of the panel. Default is NULL.

xlab

A character string specifying the x-axis label.

ylab

A character string specifying the y-axis label.

verbose

Whether to print the message. Default is TRUE.

See also

DEtestPlot, RunDEtest, VolcanoPlot, DEtestRingPlot

Examples

data(pancreas_sub)
pancreas_sub <- standard_scop(pancreas_sub)
pancreas_sub <- RunDEtest(
  pancreas_sub,
  group.by = "CellType",
  only.pos = FALSE
)
DEtestManhattanPlot(
  pancreas_sub,
  group.by = "CellType"
)