R/plot_marker_express.R
plot_marker_express.Rd
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
)
SummarizedExperiment-class object
A data.frame()
generated by get_mean_ratio()
and/or
findMarkers_1vAll()
.
A character()
target cell type to plot markers for
An integer(1)
of number of markers you'd like to plot
The character(1)
name of column to rank genes by in
stats
.
The character(1)
name of column containing annotation in
stats
.
The character(1)
name of column containing gene name in
stats
should be the same syntax as rownames(sce)
.
The character(1)
name of colData()
column containing
cell type for sce
data. It should match cellType.target
in stats
.
A named character(1)
vector that contains a color pallet
matching the cell_type
values.
A logical(1)
indicating whether to plot points over the
violin, defaults to FALSE
as these often become over plotted and quite
large (especially when saved as PDF).
An integer(1)
specifying the number of columns for the facet in
the final plot. Defaults to 2.
A ggplot2
object created with plot_gene_express()
. It is
a scater::plotExpression()
style violin plot for selected marker genes.
Other expression plotting functions:
plot_gene_express()
,
plot_marker_express_ALL()
,
plot_marker_express_List()
## Download the processed study data from
## <https://github.com/LieberInstitute/Human_DLPFC_Deconvolution>.
if (!exists("sce_DLPFC_example")) sce_DLPFC_example <- fetch_deconvo_data("sce_DLPFC_example")
#> 2024-10-31 13:27:15.118728 loading file /github/home/.cache/R/BiocFileCache/66141272054e_sce_DLPFC_example.Rdata%3Frlkey%3Dv3z4u8ru0d2y12zgdl1az07q9%26st%3D1dcfqc1i%26dl%3D1
## load example marker stats
data("marker_test")
## Plot the top markers for Astrocytes
plot_marker_express(
sce = sce_DLPFC_example,
stat = marker_test,
cellType_col = "cellType_broad_hc",
cell_type = "Astro",
gene_col = "gene"
)