NEWS.md
proteinatlas_heatmap() new arguments:
row_split to fix error when supplying both row_split and row_filter. Previously, rows could not be filtered and split, because the row_split was passed via ... and needs to be subsetted prior to passing along to Heatmap(). Now row_split is a formal argument and can be subsetted consistent with the expression matrix used in the heatmap.return_type with values "heatmap" to return the Heatmap; "list" to return a list that contains the data matrix used in the heatmap, the Heatmap itself, and other useful objects.left_annotation is an optional argument used when gene_im is not supplied, and you want to supply a specific left annotation to display in its place.proteinatlas_heatmap() new argument gene_im_colors for custom color ranges. Also gene_im data is expected to have values c(-1, 0, 1) instead of just c(0, 1) previously. Also the gene_im color legend is displayed by default.pajam_shiny_ui() fixed a simple typo in selected_genes that defines the initial starting set of genes displayed in the shiny app.'launch_pajam() via pajam_shiny_ui() will honor the value of selected_genes if defined in the global environment .GlobalEnv, otherwise it will use the default set of genes.launch_pajam() launches an R-shiny app, to help navigate the data. The app uses really nice interactive features from the ComplexHeatmap package.proteinatlas_heatmap() the main function which creates a heatmap using ComplexHeatmap::Heatmap().proteinatlas_expr_fdb11 is the central expression data matrix used for the heatmap.proteinatlas_genesets_fdb11 is a list of useful genesets that can be used as annotations beside heatmap rows.