Visualize Markers — MarkersPlot • scplotter

Plot markers, typically identified by Seurat::FindMarkers() or Seurat::FindAllMarkers().

Usage

MarkersPlot(
  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),
  ...
)

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.

...

Additional arguments passed to specific plotting functions. See Details.

Value

A ggplot object or a list of ggplot objects if not merged.

Details

Additional arguments passed to specific plotting functions:

For heatmap_log2fc, heatmap_pct, dot_log2fc, and dot_pct, the arguments will be passed to plotthis::Heatmap()
For violin, "box", "bar", "ridge" and "dot", the arguments will be passed to FeatureStatPlot()
For volcano, volcano_log2fc, volcano_pct, the arguments will be passed to plotthis::VolcanoPlot()
For jitter, jitter_log2fc, jitter_pct, the arguments will be passed to plotthis::JitterPlot()

Examples

# \donttest{
data(pancreas_sub)
markers <- Seurat::FindMarkers(pancreas_sub,
 group.by = "Phase", ident.1 = "G2M", ident.2 = "G1")
#> Warning: The `slot` argument of `GetAssayData()` is deprecated as of SeuratObject 5.0.0.
#> ℹ Please use the `layer` argument instead.
#> ℹ The deprecated feature was likely used in the Seurat package.
#>   Please report the issue at <https://github.com/satijalab/seurat/issues>.
#> Warning: `PackageCheck()` was deprecated in SeuratObject 5.0.0.
#> ℹ Please use `rlang::check_installed()` instead.
#> ℹ The deprecated feature was likely used in the Seurat package.
#>   Please report the issue at <https://github.com/satijalab/seurat/issues>.
#> For a (much!) faster implementation of the Wilcoxon Rank Sum Test,
#> (default method for FindMarkers) please install the presto package
#> --------------------------------------------
#> install.packages('devtools')
#> devtools::install_github('immunogenomics/presto')
#> --------------------------------------------
#> After installation of presto, Seurat will automatically use the more 
#> efficient implementation (no further action necessary).
#> This message will be shown once per session
allmarkers <- Seurat::FindAllMarkers(pancreas_sub)  # seurat_clusters
#> Calculating cluster 0
#> Calculating cluster 1
#> Calculating cluster 2
#> Calculating cluster 3
#> Calculating cluster 4
#> Calculating cluster 5
#> Calculating cluster 6

MarkersPlot(markers)

MarkersPlot(markers, x_cutoff = 2)

MarkersPlot(allmarkers,
    subset_by = "cluster", ncol = 2, subset_as_facet = TRUE)

MarkersPlot(markers, plot_type = "volcano_pct", flip_negative = TRUE)


MarkersPlot(allmarkers, plot_type = "jitter", subset_by = "cluster")

MarkersPlot(allmarkers, plot_type = "jitter_pct",
    subset_by = "cluster", add_hline = 0, shape = 16)


MarkersPlot(allmarkers, plot_type = "heatmap_log2fc", subset_by = "cluster")

MarkersPlot(allmarkers, plot_type = "heatmap_pct", subset_by = "cluster",
    cutoff = 0.05)


MarkersPlot(allmarkers, plot_type = "dot_log2fc", subset_by = "cluster",
    add_reticle = TRUE)


MarkersPlot(allmarkers, object = pancreas_sub, plot_type = "heatmap",
   columns_split_by = "CellType",
   comparison_by = "cluster:seurat_clusters")
#> Warning: Layer counts isn't present in the assay object; returning NULL


# Suppose we did a DE between g1 and g2 in each cluster
allmarkers$comparison <- "g1:g2"
MarkersPlot(allmarkers, object = pancreas_sub, plot_type = "heatmap",
   comparison_by = "Phase", subset_by = "cluster:seurat_clusters")
#> Warning: Layer counts isn't present in the assay object; returning NULL

MarkersPlot(allmarkers, object = pancreas_sub, plot_type = "dot",
   comparison_by = "Phase", subset_by = "cluster:seurat_clusters")
#> Warning: Layer counts isn't present in the assay object; returning NULL


MarkersPlot(allmarkers, object = pancreas_sub, plot_type = "violin", select = 3,
   comparison_by = "Phase", subset_by = "cluster:seurat_clusters")
#> Warning: Layer counts isn't present in the assay object; returning NULL


MarkersPlot(allmarkers, object = pancreas_sub, plot_type = "box", select = 3,
   comparison_by = "Phase", subset_by = "cluster:seurat_clusters")
#> Warning: Layer counts isn't present in the assay object; returning NULL


MarkersPlot(allmarkers, object = pancreas_sub, plot_type = "ridge", select = 2,
   comparison_by = "Phase", subset_by = "cluster:seurat_clusters",
   ncol = 2)
#> Warning: Layer counts isn't present in the assay object; returning NULL
#> Picking joint bandwidth of 0.265
#> Picking joint bandwidth of 0.155
#> Picking joint bandwidth of 0.153
#> Picking joint bandwidth of 0.322
#> Picking joint bandwidth of 0.222
#> Picking joint bandwidth of 0.246
#> Picking joint bandwidth of 0.326
#> Picking joint bandwidth of 0.464
#> Picking joint bandwidth of 0.307
#> Picking joint bandwidth of 0.222
#> Picking joint bandwidth of 0.306
#> Picking joint bandwidth of 0.32
#> Picking joint bandwidth of 0.094
#> Picking joint bandwidth of 0.464
#> Picking joint bandwidth of 0.0735
#> Picking joint bandwidth of 0.116
#> Picking joint bandwidth of 0.031
#> Picking joint bandwidth of 0.251
#> Picking joint bandwidth of 0.0355
#> Picking joint bandwidth of 0.144
#> Picking joint bandwidth of 0.202
#> Picking joint bandwidth of 0.278
#> Picking joint bandwidth of 0.28
#> Picking joint bandwidth of 0.239
#> Picking joint bandwidth of 0.0755
#> Picking joint bandwidth of 0.102
#> Picking joint bandwidth of 0.256
#> Picking joint bandwidth of 0.0748
#> Picking joint bandwidth of 0.174
#> Picking joint bandwidth of 0.201
#> Picking joint bandwidth of 0.361
#> Picking joint bandwidth of 0.381
#> Picking joint bandwidth of 0.234
#> Picking joint bandwidth of 0.351
#> Picking joint bandwidth of 0.368
#> Picking joint bandwidth of 0.512
#> Picking joint bandwidth of 0.351
#> Picking joint bandwidth of 0.267
#> Picking joint bandwidth of 0.259
#> Picking joint bandwidth of 0.515
#> Picking joint bandwidth of 0.461
#> Picking joint bandwidth of 0.362
#> Picking joint bandwidth of 0.0669
#> Picking joint bandwidth of 0.031
#> Picking joint bandwidth of 0.0314
#> Picking joint bandwidth of 0.264
#> Picking joint bandwidth of 0.327
#> Picking joint bandwidth of 0.153
#> Picking joint bandwidth of 0.187
#> Picking joint bandwidth of 0.0693
#> Picking joint bandwidth of 0.124
#> Picking joint bandwidth of 0.268
#> Picking joint bandwidth of 0.255
#> Picking joint bandwidth of 0.327
#> Picking joint bandwidth of 0.282
#> Picking joint bandwidth of 0.112
#> Picking joint bandwidth of 0.267
#> Picking joint bandwidth of 0.254
#> Picking joint bandwidth of 0.209
#> Picking joint bandwidth of 0.188
#> Picking joint bandwidth of 0.229
#> Picking joint bandwidth of 0.204
#> Picking joint bandwidth of 0.0543
#> Picking joint bandwidth of 0.0263
#> Picking joint bandwidth of 0.0421
#> Picking joint bandwidth of 0.256
#> Picking joint bandwidth of 0.196
#> Picking joint bandwidth of 0.193
#> Picking joint bandwidth of 0.18
#> Picking joint bandwidth of 0.0409
#> Picking joint bandwidth of 0.0677
#> Picking joint bandwidth of 0.0491
#> Picking joint bandwidth of 0.358
#> Picking joint bandwidth of 0.241
#> Picking joint bandwidth of 0.0658
#> Picking joint bandwidth of 0.195
#> Picking joint bandwidth of 0.468
#> Picking joint bandwidth of 0.0579
#> Picking joint bandwidth of 0.0672
#> Picking joint bandwidth of 0.185
#> Picking joint bandwidth of 0.173
#> Picking joint bandwidth of 0.0904
#> Picking joint bandwidth of 0.174
#> Picking joint bandwidth of 0.269
#> Picking joint bandwidth of 0.0588
#> Picking joint bandwidth of 0.0847
#> Picking joint bandwidth of 0.0403
#> Picking joint bandwidth of 0.51
#> Picking joint bandwidth of 0.0428
#> Picking joint bandwidth of 0.29
#> Picking joint bandwidth of 0.0428
#> Picking joint bandwidth of 0.364
#> Picking joint bandwidth of 0.09
#> Picking joint bandwidth of 0.518
#> Picking joint bandwidth of 0.285
#> Picking joint bandwidth of 0.25
#> Picking joint bandwidth of 0.259
#> Picking joint bandwidth of 0.364
#> Picking joint bandwidth of 0.265
#> Picking joint bandwidth of 0.155
#> Picking joint bandwidth of 0.153
#> Picking joint bandwidth of 0.322
#> Picking joint bandwidth of 0.222
#> Picking joint bandwidth of 0.246
#> Picking joint bandwidth of 0.326
#> Picking joint bandwidth of 0.464
#> Picking joint bandwidth of 0.307
#> Picking joint bandwidth of 0.222
#> Picking joint bandwidth of 0.306
#> Picking joint bandwidth of 0.32
#> Picking joint bandwidth of 0.094
#> Picking joint bandwidth of 0.464
#> Picking joint bandwidth of 0.0735
#> Picking joint bandwidth of 0.116
#> Picking joint bandwidth of 0.031
#> Picking joint bandwidth of 0.251
#> Picking joint bandwidth of 0.0355
#> Picking joint bandwidth of 0.144
#> Picking joint bandwidth of 0.202
#> Picking joint bandwidth of 0.278
#> Picking joint bandwidth of 0.28
#> Picking joint bandwidth of 0.239
#> Picking joint bandwidth of 0.0755
#> Picking joint bandwidth of 0.102
#> Picking joint bandwidth of 0.256
#> Picking joint bandwidth of 0.0748
#> Picking joint bandwidth of 0.174
#> Picking joint bandwidth of 0.201
#> Picking joint bandwidth of 0.361
#> Picking joint bandwidth of 0.381
#> Picking joint bandwidth of 0.234
#> Picking joint bandwidth of 0.351
#> Picking joint bandwidth of 0.368
#> Picking joint bandwidth of 0.512
#> Picking joint bandwidth of 0.351
#> Picking joint bandwidth of 0.267
#> Picking joint bandwidth of 0.259
#> Picking joint bandwidth of 0.515
#> Picking joint bandwidth of 0.461
#> Picking joint bandwidth of 0.362
#> Picking joint bandwidth of 0.0669
#> Picking joint bandwidth of 0.031
#> Picking joint bandwidth of 0.0314
#> Picking joint bandwidth of 0.264
#> Picking joint bandwidth of 0.327
#> Picking joint bandwidth of 0.153
#> Picking joint bandwidth of 0.187
#> Picking joint bandwidth of 0.0693
#> Picking joint bandwidth of 0.124
#> Picking joint bandwidth of 0.268
#> Picking joint bandwidth of 0.255
#> Picking joint bandwidth of 0.327
#> Picking joint bandwidth of 0.282
#> Picking joint bandwidth of 0.112
#> Picking joint bandwidth of 0.267
#> Picking joint bandwidth of 0.254
#> Picking joint bandwidth of 0.209
#> Picking joint bandwidth of 0.188
#> Picking joint bandwidth of 0.229
#> Picking joint bandwidth of 0.204
#> Picking joint bandwidth of 0.0543
#> Picking joint bandwidth of 0.0263
#> Picking joint bandwidth of 0.0421
#> Picking joint bandwidth of 0.256
#> Picking joint bandwidth of 0.196
#> Picking joint bandwidth of 0.193
#> Picking joint bandwidth of 0.18
#> Picking joint bandwidth of 0.0409
#> Picking joint bandwidth of 0.0677
#> Picking joint bandwidth of 0.0491
#> Picking joint bandwidth of 0.358
#> Picking joint bandwidth of 0.241
#> Picking joint bandwidth of 0.0658
#> Picking joint bandwidth of 0.195
#> Picking joint bandwidth of 0.468
#> Picking joint bandwidth of 0.0579
#> Picking joint bandwidth of 0.0672
#> Picking joint bandwidth of 0.185
#> Picking joint bandwidth of 0.173
#> Picking joint bandwidth of 0.0904
#> Picking joint bandwidth of 0.174
#> Picking joint bandwidth of 0.269
#> Picking joint bandwidth of 0.0588
#> Picking joint bandwidth of 0.0847
#> Picking joint bandwidth of 0.0403
#> Picking joint bandwidth of 0.51
#> Picking joint bandwidth of 0.0428
#> Picking joint bandwidth of 0.29
#> Picking joint bandwidth of 0.0428
#> Picking joint bandwidth of 0.364
#> Picking joint bandwidth of 0.09
#> Picking joint bandwidth of 0.518
#> Picking joint bandwidth of 0.285
#> Picking joint bandwidth of 0.25
#> Picking joint bandwidth of 0.259
#> Picking joint bandwidth of 0.364

# }