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"), 5, 10),
  outprefix = NULL,
  devpars = list(res = 100),
  more_formats = c(),
  save_code = FALSE,
  ...
)

Arguments

markers

A data frame of markers, typically identified by Seurat::FindMarkers() or Seurat::FindAllMarkers().

object

A Seurat object. Required for some plot types, see plot_type.

plot_type

Type of plot to generate. Options include:

volcano/volcano_log2fc: Volcano plot with log2 fold change on x-axis and -log10(p-value) on y-axis. If p_adjust is TRUE, -log10(adjusted p-value) is used instead.
volcano_pct: Volcano plot with difference in percentage of cells expressing the gene between two groups on x-axis and -log10(p-value) on y-axis. If p_adjust is TRUE, -log10(adjusted p-value) is used instead.
jitter/jitter_log2fc: Jitter plot of log2 fold change for each gene. The x-axis is the groups defined by subset_by, and the y-axis is log2 fold change. The size of the dots represents -log10(p-value) or -log10(adjusted p-value) if p_adjust is TRUE.
jitter_pct: Jitter plot of difference in percentage of cells expressing the gene between two groups for each gene. The x-axis is the groups defined by subset_by, and the y-axis is the difference in percentage of cells expressing the gene between two groups. The size of the dots represents -log10(p-value) or -log10(adjusted p-value) if p_adjust is TRUE.
heatmap_log2fc: Heatmap of log2 fold change for each gene across groups defined by subset_by. By specifying cutoff, The heatmap cells will be labeled with "*" for p-value < cutoff, if p_adjust is TRUE, adjusted p-value < cutoff.
heatmap_pct: Heatmap of difference in percentage of cells expressing the gene between two groups for each gene across groups defined by subset_by. By specifying cutoff, The heatmap cells will be labeled with "*" for p-value < cutoff, if p_adjust is TRUE, adjusted p-value < cutoff.
dot_log2fc: Dot plot of log2 fold change for each gene across groups defined by subset_by. The size of the dots represents -log10(p-value) or -log10(adjusted p-value) if p_adjust is TRUE.
dot_pct: Dot plot of difference in percentage of cells expressing the gene between two groups for each gene across groups defined by subset_by. The size of the dots represents -log10(p-value) or -log10(adjusted p-value) if p_adjust is TRUE.
heatmap: Heatmap of expression values for each gene across groups defined by subset_by. Requires object.
violin: Violin plot of expression values for each gene across groups defined by subset_by. Requires object.
box: Box plot of expression values for each gene across groups defined by subset_by. Requires object.
bar: Bar plot of average expression values for each gene across groups defined by subset_by. Requires object.
ridge: Ridge plot of expression values for each gene across groups defined by subset_by. Requires object.
dot: Dot plot of expression values for each gene across groups defined by subset_by. Requires object.

subset_by

A column in markers indicating where the markers are identified from, e.g., cluster or condition. If object is provided, you can provide the corresponding metadata column in subset_by to merge the markers with the object's metadata, using : as separator. For example, if the markers are identified from different clusters (identified by FindAllMarkers), and the object's ident column is "RNA_snn_res.0.8", you can set subset_by = "cluster:RNA_snn_res.0.8". Note that for other columns to be merged, only the first value of each group defined by subset_by will be used. For some plots, this is used to split the markers into multiple plots, e.g., one plot for each cluster. See plot_type for details.

subset_as_facet

Logical, whether to facet the plots by subset_by if applicable.

comparison_by

The metadata column in markers indicating the comparion. When visualizing the expression values, this column should also be in the object's metadata. The values of this column should either a single value, indicating the comparison is between this group and all other cells (in the subset), Similar as subset_by, you can provide the corresponding object metadata column by using : as separator. If NULL, all markers are treated as from one comparison.

p_adjust

Logical, whether to use adjusted p-value for plots that involve p-values. Default is TRUE.

cutoff

Numeric, p-value or adjusted p-value cutoff to label significance in heatmap plots. Default is NULL, no cutoff.

order_by

A string of expression to order the markers within each group defined by subset_by. In addition to the columns in markers, you can also use the columns from the object's metadata if object is provided. The object's metadata will be merged with markers by subset_by. Be carefull that only the first value of other columns will be used.

select

Number of top markers (ordered by order_by) to select for each group defined by subset_by or a string of expression to filter markers. It will be evaluated by dplyr::filter(). For volcano, volcano_log2fc, volcano_pct, jitter, jitter_log2fc, and jitter_pct plots, the selected markers will be labeled in the plot. FOr other plot types, only the selected markers will be plotted. Default is 5 for volcano, volcano_log2fc, volcano_pct, jitter, jitter_log2fc, jitter_pct, and 10 for other plot types.

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

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 0.252
#> Picking joint bandwidth of 0.283
#> Picking joint bandwidth of 0.0311
#> Picking joint bandwidth of 0.0338
#> Picking joint bandwidth of 0.031
#> Picking joint bandwidth of 0.382
#> Picking joint bandwidth of 0.196
#> Picking joint bandwidth of 0.0675
#> Picking joint bandwidth of 0.133
#> Picking joint bandwidth of 0.537
#> Picking joint bandwidth of 0.3
#> Picking joint bandwidth of 0.505
#> Picking joint bandwidth of 0.505
#> Picking joint bandwidth of 0.283
#> Picking joint bandwidth of 0.308
#> Picking joint bandwidth of 0.326
#> Picking joint bandwidth of 0.305
#> Picking joint bandwidth of 0.398
#> Picking joint bandwidth of 0.455
#> Picking joint bandwidth of 0.135
#> Picking joint bandwidth of 0.526
#> Picking joint bandwidth of 0.526
#> Picking joint bandwidth of 0.518
#> Picking joint bandwidth of 0.353
#> 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 0.252
#> Picking joint bandwidth of 0.283
#> Picking joint bandwidth of 0.0311
#> Picking joint bandwidth of 0.0338
#> Picking joint bandwidth of 0.031
#> Picking joint bandwidth of 0.382
#> Picking joint bandwidth of 0.196
#> Picking joint bandwidth of 0.0675
#> Picking joint bandwidth of 0.133
#> Picking joint bandwidth of 0.537
#> Picking joint bandwidth of 0.3
#> Picking joint bandwidth of 0.505
#> Picking joint bandwidth of 0.505
#> Picking joint bandwidth of 0.283
#> Picking joint bandwidth of 0.308
#> Picking joint bandwidth of 0.326
#> Picking joint bandwidth of 0.305
#> Picking joint bandwidth of 0.398
#> Picking joint bandwidth of 0.455
#> Picking joint bandwidth of 0.135
#> Picking joint bandwidth of 0.526
#> Picking joint bandwidth of 0.526
#> Picking joint bandwidth of 0.518
#> Picking joint bandwidth of 0.353
#> 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