pajam: Protein Atlas data and visualization

#' Protein Atlas expression data version fdb11
#' 
#' Protein Atlas expression data version fdb11
#' 
#' This data contains the expression profile data from
#' https://proteinatlas.org for each gene/protein provided
#' in version fdb11.
#' 
#' @format `matrix` of numeric values, following their normalization
#'    methodology. The rownames indicate official Entrez gene symbols,
#'    and the colnames indicate biological samples. The colnames
#'    include a suffix indicating the type of sample, and include:
#'    `"Tissue"`, `"Blood"`, `"Brain"`, and `"Cell"`. Note that
#'    `"Blood"` and `"Brain"` samples may also be included in the
#'    overall `"Tissue"` samples.
#' 
#' @family pajam data
#' 
"proteinatlas_expr_fdb11"

#' Protein Atlas useful genesets for visualization
#' 
#' Protein Atlas useful genesets for visualization
#' 
#' This object includes a list of genesets in the form of
#' character vectors of rownames aligned with
#' `proteinatlas_expr_fdb11`. The genesets are some useful
#' annotations for visualization that include:
#' 
#' * `"Plasma"` - found in circulating blood plasma
#' * `"secreted_proteins"` - secreted proteins
#' * `"membrane_proteins"` - membrane-bound proteins
#' * `"FDA"` - gene targets of FDA-approved drugs
#' * `"NOT_membrane_secreted"` - non-membrane and non-secreted proteins (intracellular)
#' * `"TFs"` - transcription factors
#' * `"HKs"` - housekeeper genes
#' * `"rna_lymphoid"` - RNA-lymphoid associated genes
#' 
#' The annotations are not intended to be fully exhaustive,
#' but are intended to represent some useful annotations
#' not necessarily associated directly with the biological
#' function of each gene/protein. For example, it may be useful
#' to see whether most up-regulated proteins are secreted or
#' intracellular, or perhaps most up-regulated gene transcripts
#' are transcription factors and are not secreted.
#' 
#' @format `list` of `character vector`, whose values match
#'    `rownames(proteinatlas_expr_fdb11)`.
#' 
#' @examples
#' use_im <- c("secreted_proteins",
#'    "membrane_proteins",
#'    "NOT_membrane_secreted",
#'    "TFs");
#' proteinatlas_im <- list2im_opt(proteinatlas_genesets_fdb11[use_im]);
#' test_genes <- c("DKK1","DKK4","CXCL12","IL6R","MET",
#'    "HK2","FTL","FTH1","STAT1","STAT3","CDKN1B");
#' 
#' proteinatlas_heatmap(genes=test_genes,
#'    type="Blood",
#'    centered=TRUE,
#'    gene_im=proteinatlas_im);
#' 
#' proteinatlas_heatmap(genes=test_genes,
#'    type="Blood",
#'    centered=TRUE,
#'    column_filter=4,
#'    row_cex=0.8,
#'    column_names_max_height=grid::unit(12, "cm"),
#'    gene_im=proteinatlas_im);
#' 
#' @family pajam data
#' 
"proteinatlas_genesets_fdb11"