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Gene expression in testis cells

Source: R/testis_expression.R
testis_expression.Rd

Plots a heatmap of genes expression in the different types of testis cells, using scRNAseq data from "The adult human testis transcriptional cell atlas" (Guo et al. 2018)

Usage

testis_expression(
  cells = c("all", "germ_cells", "somatic_cells", "SSC", "Spermatogonia",
    "Early_spermatocyte", "Late_spermatocyte", "Round_spermatid", "Elongated_spermatid",
    "Sperm1", "Sperm2", "Macrophage", "Endothelial", "Myoid", "Sertoli", "Leydig"),
  genes = NULL,
  include_CTP = FALSE,
  scale_lims = NULL,
  values_only = FALSE
)

Arguments

cells

character defining the testis cell types to be plotted. Can be "germ_cells", "somatic_cells", "all" (default), or any or a combination of "SSC", "Spermatogonia", "Early_spermatocyte", "Late_spermatocyte", "Round_spermatid", "Elongated_spermatid", "Sperm1", "Sperm2", "Macrophage", "Endothelial", "Myoid", "Sertoli", "Leydig".

genes

character naming the selected genes. The default value, NULL, takes all CT (specific) genes.

include_CTP

logical(1) If TRUE, CTP genes are included. (FALSE by default).

scale_lims

vector of length 2 setting the lower and upper limits of the heatmap colorbar. By default, the lower limit is 0, and the upper limit corresponds to the third quartile of the logcounts values.

values_only

logical(1). If TRUE, the function will return the SingleCellExperiment instead of the heatmap. Default is FALSE.

Value

A heatmap of selected CT genes expression in single cells from adult testis. If values_only = TRUE, a SingleCellExperiment is returned instead.

Examples

if (FALSE) { # \dontrun{
testis_expression(cells = "germ_cells",
                  genes = c("MAGEA1", "MAGEA3", "MAGEA4"))
} # }