View source: R/plot_marker_express.R
plot_marker_express | R Documentation |
This function plots the top n marker genes for a specified cell type based off of
the stats
table from get_mean_ratio2()
.
The gene expression is plotted as violin plot with plot_gene_express
and adds
annotations to each plot.
plot_marker_express(
sce,
stats,
cell_type,
n_genes = 4,
rank_col = "MeanRatio.rank",
anno_col = "MeanRatio.anno",
gene_col = "gene",
cellType_col = "cellType",
color_pal = NULL,
plot_points = FALSE,
ncol = 2
)
sce |
SummarizedExperiment-class object |
stats |
A |
cell_type |
A |
n_genes |
An |
rank_col |
The |
anno_col |
The |
gene_col |
The |
cellType_col |
The |
color_pal |
A named |
plot_points |
A logical indicating whether to plot points over the violin,
defaults to |
ncol |
= Number of columns for the facet in the final plot. Defaults to 2. |
plotExpression style violin plot for selected marker genes
Other expression plotting functions:
plot_gene_express()
,
plot_marker_express_ALL()
,
plot_marker_express_List()
if (!exists("sce_DLPFC_example")) sce_DLPFC_example <- fetch_deconvo_data("sce_DLPFC_example")
## plot the top markers for Astrocytes in
plot_marker_express(
sce = sce_DLPFC_example,
stat = marker_test,
cellType_col = "cellType_broad_hc",
cell_type = "Astro",
gene_col = "gene"
)
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