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Gene expression in different human cell types

Source: R/HPA_cell_type_expression.R
HPA_cell_type_expression.Rd

Plots a heatmap of genes expression in the different human cell types based on scRNAseq data obtained from the Human Protein Atlas (https://www.proteinatlas.org)

Usage

HPA_cell_type_expression(
  genes = NULL,
  units = c("scaled", "TPM", "log_TPM"),
  include_CTP = FALSE,
  scale_lims = NULL,
  values_only = FALSE
)

Arguments

genes

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

units

character(1) with expression values unit. Can be "TPM", "log_TPM" (log(TPM + 1)) or "scaled" (scaled TPM values). Default is "scaled".

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.

values_only

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

Value

A heatmap of selected CT genes expression in different human cell types. If values_only = TRUE, a SummarizedExperiment instead of the heatmap is returned instead.

Examples


HPA_cell_type_expression(
    genes = NULL, units = "scaled", scale_lims = NULL,
    values_only = FALSE)
#> see ?CTdata and browseVignettes('CTdata') for documentation
#> loading from cache
#> Warning: 29 out of 146 names invalid: KAZN-AS1, NFIA-AS1, LRRC52-AS1, LINC01249,
#> THORLNC, LINC01206, LINC02475, LINC02377, SLC7A11-AS1, LINC01098,
#> LINC01511, LINC02241, LINC02228, LINC03004, SEC61G-DT, GTF2I-AS1,
#> LINC00200, LINC02663, LINC01518, LINC02750, TMEM132D-AS1, FAM230C,
#> LINC01193, LINC01413, FLJ36000, LINC00470, LINC02864, DSCR8,
#> MAGEA4-AS1.
#> See the manual page for valid types.

HPA_cell_type_expression(
    genes = c("MAGEA1", "MAGEA3", "MAGEA4"),
    units = "TPM", scale_lims = c(0, 50),
    values_only = FALSE)
#> see ?CTdata and browseVignettes('CTdata') for documentation
#> loading from cache