Visualize DEGs

Visualize differentially expressed genes

Usage

VizDEGs(
  markers,
  object = NULL,
  plot_type = c("volcano", "volcano_log2fc", "volcano_pct", "jitter", "jitter_log2fc",
    "jitter_pct", "heatmap_log2fc", "heatmap_pct", "dot_log2fc", "dot_pct", "heatmap",
    "violin", "box", "bar", "ridge", "dot"),
  subset_by = NULL,
  subset_as_facet = FALSE,
  comparison_by = NULL,
  p_adjust = TRUE,
  cutoff = NULL,
  order_by = NULL,
  select = ifelse(plot_type %in% c("volcano", "volcano_log2fc", "volcano_pct",
    "jitter", "jitter_log2fc", "jitter_pct", "heatmap_log2fc", "heatmap_pct"), 5, 10),
  outprefix = NULL,
  devpars = list(res = 100),
  more_formats = c(),
  save_code = FALSE,
  ...
)

Arguments

markers

A data frame of differential expression results, typically the output of Seurat::FindMarkers() or Seurat::FindAllMarkers(). Must contain columns "gene" (or gene symbols as rownames), "p_val", and "avg_log2FC". For percentage-based plots (volcano_pct, jitter_pct, heatmap_pct, dot_pct), columns "pct.1" and "pct.2" are also required.

object

A Seurat object. Required for expression-based plot types: "heatmap", "violin", "box", "bar", "ridge", and "dot". Not used for DE summary plot types. Default: NULL.

plot_type

The type of plot to generate. One of "volcano", "volcano_log2fc", "volcano_pct", "jitter", "jitter_log2fc", "jitter_pct", "heatmap_log2fc", "heatmap_pct", "dot_log2fc", "dot_pct", "heatmap", "violin", "box", "bar", "ridge", or "dot". See Description for details on each type.

subset_by

A column name in markers indicating the grouping from which each marker was identified (e.g., the cluster column from FindAllMarkers()). Supports the "marker_column:metadata_column" syntax for linking to Seurat object metadata (see Metadata column mapping section). For jitter and DE heatmap/dot plot types, subset_by is required and defines the x-axis or column groups. For expression plot types, subset_by controls faceting or splitting. Default: NULL.

subset_as_facet

Logical. If TRUE, facet the plot by subset_by groups instead of splitting into separate plots. Most useful for expression plot types. For volcano plots, controls whether faceting or split_by dispatch is used. Default: FALSE.

comparison_by

A column name in markers indicating the comparison (e.g., "g1:g2" for a pairwise comparison, or a single group name for one-vs-rest). Required for expression-based plot types ("heatmap", "violin", "box", "bar", "ridge", "dot"). Supports the "marker_column:metadata_column" syntax (see Metadata column mapping section). If the comparison values contain a colon (e.g., "G2M:G1"), the two groups on either side of the colon are used to subset the object. If only a single group is present, a one-vs-other comparison is assumed. Default: NULL.

p_adjust

Logical. If TRUE (default), use adjusted p-value (p_val_adj column) for significance calculations and y-axis transformations. If FALSE, use raw p-value (p_val column).

cutoff

Numeric. The p-value (or adjusted p-value, depending on p_adjust) threshold for labeling significance. For volcano plots, sets y_cutoff. For heatmap-based DE plots (heatmap_log2fc, heatmap_pct), controls which cells receive significance marks. Default: NULL (no cutoff; defaults to 0.05 for volcano plots).

order_by

A string expression to order markers by (evaluated with dplyr::arrange()). Can reference columns in markers as well as columns from the object metadata (when object is provided and subset_by enables merging). Only the first value of merged metadata columns is used. Example: "desc(avg_log2FC)". The ordering affects which markers are selected when select is numeric. Default: NULL.

select

How to select markers for labeling or display. See Marker selection and filtering section for full details.

Numeric: Top N markers per subset_by group (default: 5 for volcano/jitter types, 10 for others).
Character expression: Filter condition for dplyr::filter().
Character vector: Multiple filter expressions; those containing the subset_by column name filter the overall data, others filter within remaining data.

outprefix

Prefix of the output file

devpars

List of parameters to save the plot

more_formats

Additional formats to save the plot in addition to 'png'

save_code

Whether to save the code to reproduce the plot

...

Arguments passed on to scplotter::MarkersPlot

show_labels: Logical. For heatmap_log2fc and heatmap_pct plot types only. If TRUE, display numeric values in heatmap cells. When combined with cutoff, both values and significance marks are shown. Default: FALSE.
sig_mark: Character. The symbol or compound mark used to annotate statistically significant cells in heatmap_log2fc and heatmap_pct plots. Must be a valid ComplexHeatmap mark: single characters ("-", "|", "+", "/", "\\", "x", "o") or compound marks ("[*]", "<*>", "(*)", "{*}"). Note that "*" conflicts with show_labels = TRUE because both use the label layer — use a compound mark instead. Default: "*".

Value

A ggplot object if 'outprefix' is NULL, otherwise, save the plot to the output directory

Examples

# \donttest{
degs <- RunSeuratDEAnalysis(scplotter::pancreas_sub, "SubCellType")
VizDEGs(degs, plot_type = "volcano_pct")

VizDEGs(degs, plot_type = "volcano_log2fc")

VizDEGs(degs, plot_type = "jitter_log2fc", subset_by = "SubCellType")

VizDEGs(degs,
    plot_type = "heatmap_log2fc", cutoff = 0.05,
    select = 5, subset_by = "SubCellType"
)


# Visualize expression of the top DEGs
# Suppose we did comparison between G2M and S phase in each SubCellType
degs$Phase <- "G2M:S"

VizDEGs(degs,
    object = scplotter::pancreas_sub, plot_type = "violin",
    select = 2, comparison_by = "Phase", subset_by = "SubCellType"
)
#> Warning: Layer counts isn't present in the assay object; returning NULL
#> Warning: Groups with fewer than two datapoints have been dropped.
#> ℹ Set `drop = FALSE` to consider such groups for position adjustment purposes.
#> Warning: Groups with fewer than two datapoints have been dropped.
#> ℹ Set `drop = FALSE` to consider such groups for position adjustment purposes.
#> Warning: Groups with fewer than two datapoints have been dropped.
#> ℹ Set `drop = FALSE` to consider such groups for position adjustment purposes.
#> Warning: Groups with fewer than two datapoints have been dropped.
#> ℹ Set `drop = FALSE` to consider such groups for position adjustment purposes.
#> Warning: Groups with fewer than two datapoints have been dropped.
#> ℹ Set `drop = FALSE` to consider such groups for position adjustment purposes.
#> Warning: Groups with fewer than two datapoints have been dropped.
#> ℹ Set `drop = FALSE` to consider such groups for position adjustment purposes.
#> Warning: Groups with fewer than two datapoints have been dropped.
#> ℹ Set `drop = FALSE` to consider such groups for position adjustment purposes.
#> Warning: Groups with fewer than two datapoints have been dropped.
#> ℹ Set `drop = FALSE` to consider such groups for position adjustment purposes.
#> Warning: Groups with fewer than two datapoints have been dropped.
#> ℹ Set `drop = FALSE` to consider such groups for position adjustment purposes.
#> Warning: Groups with fewer than two datapoints have been dropped.
#> ℹ Set `drop = FALSE` to consider such groups for position adjustment purposes.
#> Warning: Groups with fewer than two datapoints have been dropped.
#> ℹ Set `drop = FALSE` to consider such groups for position adjustment purposes.
#> Warning: Groups with fewer than two datapoints have been dropped.
#> ℹ Set `drop = FALSE` to consider such groups for position adjustment purposes.
#> Warning: Groups with fewer than two datapoints have been dropped.
#> ℹ Set `drop = FALSE` to consider such groups for position adjustment purposes.
#> Warning: Groups with fewer than two datapoints have been dropped.
#> ℹ Set `drop = FALSE` to consider such groups for position adjustment purposes.
#> Warning: Groups with fewer than two datapoints have been dropped.
#> ℹ Set `drop = FALSE` to consider such groups for position adjustment purposes.
#> Warning: Groups with fewer than two datapoints have been dropped.
#> ℹ Set `drop = FALSE` to consider such groups for position adjustment purposes.
#> Warning: Groups with fewer than two datapoints have been dropped.
#> ℹ Set `drop = FALSE` to consider such groups for position adjustment purposes.
#> Warning: Groups with fewer than two datapoints have been dropped.
#> ℹ Set `drop = FALSE` to consider such groups for position adjustment purposes.
#> Warning: Groups with fewer than two datapoints have been dropped.
#> ℹ Set `drop = FALSE` to consider such groups for position adjustment purposes.
#> Warning: Groups with fewer than two datapoints have been dropped.
#> ℹ Set `drop = FALSE` to consider such groups for position adjustment purposes.
#> Warning: Groups with fewer than two datapoints have been dropped.
#> ℹ Set `drop = FALSE` to consider such groups for position adjustment purposes.
#> Warning: Groups with fewer than two datapoints have been dropped.
#> ℹ Set `drop = FALSE` to consider such groups for position adjustment purposes.
#> Warning: Groups with fewer than two datapoints have been dropped.
#> ℹ Set `drop = FALSE` to consider such groups for position adjustment purposes.
#> Warning: Groups with fewer than two datapoints have been dropped.
#> ℹ Set `drop = FALSE` to consider such groups for position adjustment purposes.
#> Warning: Groups with fewer than two datapoints have been dropped.
#> ℹ Set `drop = FALSE` to consider such groups for position adjustment purposes.
#> Warning: Groups with fewer than two datapoints have been dropped.
#> ℹ Set `drop = FALSE` to consider such groups for position adjustment purposes.
#> Warning: Groups with fewer than two datapoints have been dropped.
#> ℹ Set `drop = FALSE` to consider such groups for position adjustment purposes.
#> Warning: Groups with fewer than two datapoints have been dropped.
#> ℹ Set `drop = FALSE` to consider such groups for position adjustment purposes.
#> Warning: Groups with fewer than two datapoints have been dropped.
#> ℹ Set `drop = FALSE` to consider such groups for position adjustment purposes.
#> Warning: Groups with fewer than two datapoints have been dropped.
#> ℹ Set `drop = FALSE` to consider such groups for position adjustment purposes.
#> Warning: Groups with fewer than two datapoints have been dropped.
#> ℹ Set `drop = FALSE` to consider such groups for position adjustment purposes.
#> Warning: Groups with fewer than two datapoints have been dropped.
#> ℹ Set `drop = FALSE` to consider such groups for position adjustment purposes.

VizDEGs(degs,
    object = scplotter::pancreas_sub, plot_type = "box",
    select = 2, comparison_by = "Phase", subset_by = "SubCellType"
)
#> Warning: Layer counts isn't present in the assay object; returning NULL

VizDEGs(degs,
    object = scplotter::pancreas_sub, plot_type = "bar",
    select = 2, comparison_by = "Phase", subset_by = "SubCellType"
)
#> Warning: Layer counts isn't present in the assay object; returning NULL

VizDEGs(degs,
    object = scplotter::pancreas_sub, plot_type = "ridge",
    select = 1, comparison_by = "Phase", subset_by = "SubCellType"
)
#> Warning: Layer counts isn't present in the assay object; returning NULL
#> Picking joint bandwidth of 0.283
#> Picking joint bandwidth of 0.252
#> Picking joint bandwidth of 0.196
#> Picking joint bandwidth of 0.0311
#> Picking joint bandwidth of 0.0338
#> Picking joint bandwidth of 0.382
#> Picking joint bandwidth of 0.0675
#> Picking joint bandwidth of 0.031
#> Picking joint bandwidth of 0.537
#> Picking joint bandwidth of 0.133
#> Picking joint bandwidth of 0.308
#> Picking joint bandwidth of 0.3
#> Picking joint bandwidth of 0.505
#> Picking joint bandwidth of 0.283
#> Picking joint bandwidth of 0.326
#> Picking joint bandwidth of 0.505
#> Picking joint bandwidth of 0.398
#> Picking joint bandwidth of 0.305
#> Picking joint bandwidth of 0.518
#> Picking joint bandwidth of 0.455
#> Picking joint bandwidth of 0.135
#> Picking joint bandwidth of 0.526
#> Picking joint bandwidth of 0.353
#> Picking joint bandwidth of 0.526
#> Picking joint bandwidth of NaN
#> Picking joint bandwidth of NaN
#> Picking joint bandwidth of NaN
#> Picking joint bandwidth of NaN
#> Picking joint bandwidth of NaN
#> Picking joint bandwidth of NaN
#> Picking joint bandwidth of NaN
#> Picking joint bandwidth of NaN
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's fill values.
#> Picking joint bandwidth of 0.283
#> Picking joint bandwidth of 0.252
#> Picking joint bandwidth of 0.196
#> Picking joint bandwidth of 0.0311
#> Picking joint bandwidth of 0.0338
#> Picking joint bandwidth of 0.382
#> Picking joint bandwidth of 0.0675
#> Picking joint bandwidth of 0.031
#> Picking joint bandwidth of 0.537
#> Picking joint bandwidth of 0.133
#> Picking joint bandwidth of 0.308
#> Picking joint bandwidth of 0.3
#> Picking joint bandwidth of 0.505
#> Picking joint bandwidth of 0.283
#> Picking joint bandwidth of 0.326
#> Picking joint bandwidth of 0.505
#> Picking joint bandwidth of 0.398
#> Picking joint bandwidth of 0.305
#> Picking joint bandwidth of 0.518
#> Picking joint bandwidth of 0.455
#> Picking joint bandwidth of 0.135
#> Picking joint bandwidth of 0.526
#> Picking joint bandwidth of 0.353
#> Picking joint bandwidth of 0.526
#> Picking joint bandwidth of NaN
#> Picking joint bandwidth of NaN
#> Picking joint bandwidth of NaN
#> Picking joint bandwidth of NaN
#> Picking joint bandwidth of NaN
#> Picking joint bandwidth of NaN
#> Picking joint bandwidth of NaN
#> Picking joint bandwidth of NaN
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's fill values.

VizDEGs(degs,
    object = scplotter::pancreas_sub, plot_type = "heatmap",
    cluster_columns = FALSE, comparison_by = "Phase", subset_by = "SubCellType"
)
#> Warning: Layer counts isn't present in the assay object; returning NULL

VizDEGs(degs,
    object = scplotter::pancreas_sub, plot_type = "dot",
    select = 1, comparison_by = "Phase", subset_by = "SubCellType"
)
#> Warning: Layer counts isn't present in the assay object; returning NULL

# }

Usage

Arguments

Value

See also

Examples