NEWS.md

In jmw86069/pajam: Protein Atlas data and visualization

pajam 0.0.5.900

changes to existing functions, and one bug fix

• proteinatlas_heatmap() was updated to call the correct function from the jamma package. The dependency on jamma was updated to version 0.0.19.900.

pajam 0.0.4.900

changes to existing functions, and one bug fix

• 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.

pajam 0.0.3.900

changes to existing functions

• 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 0.0.2.900

changes to existing functions

• 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.

pajam 0.0.1.900

new functions

• launch_pajam() launches an R-shiny app, to help navigate the data. The app uses really nice interactive features from the ComplexHeatmap package.

pajam 0.0.0.900

initial release

• 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.

jmw86069/pajam documentation built on Feb. 6, 2022, 1:30 p.m.