v2.1: support for visualising subsets of cells

Minor update to v2.1 to support the visualization of subsets of cells

Updates include:

• Ability to visualize subsets of cells
  --- Users can now subset cells by any categorical metadata e.g. visualize only certain libraries or clusters
  --- For dimension reduction plots, cells that are not selected will still be displayed as very light grey in the background
  --- For violin/boxplots & proportion plots & bubbleplot/heatmaps, users can also subset cells
  --- Added "Select all" and "Deselect all" buttons for user convenience
  --- Users can also choose to disable this function by specifying this new argumentenableSubset = FALSE in the makeShinyApp or makeShinyCodesMulti function (related to issue #15)
  

• Bugfix and updates to improve user experience
  --- Fix bug where short gene names cannot be searched (related to issue #19)
  --- Add an argument defPtSiz = 1.25 in the makeShinyApp and makeShinyCodesMulti function to specify default point sizes (related to issue #18)
  --- Updates to support the latest version of SCE (related to #11 #12 #17)

v2.0: bioinformatics publication release

Major update to v2.0 following publication on Bioinformatics journal

Updates include:

• Inclusion of cluster/metadata labels in Dimension Reduction plots
• Inclusion of coexpression plots
• Inclusion of proportion plots
• Inclusion of cell number / statistics tables
• Inclusion of ability to subset cells in Dimension Reduction plots

v1.1: Support for major single-cell data formats

Minor update to v1.1

Updates include:

• Support for h5ad / loom file formats (on top of Seurat and SCE)

v1.0: biorxiv release

First release v1.0 following biorxiv preprint

Features include:

• Plotting cell metadata and gene expression side-by-side on Dimension Reduction plots
• Violin plot / box plot of cell metadata or gene expression
• Bubbleplot / heatmap of multiple gene expression