auto_annotate: Automatically format an annotation file. From...

In AllenInstitute/L5_VEN:

Automatically format an annotation file. From libary(scrattch.io)

Description

This takes an anno file as input at any stage and properly annotates it for compatability with shiny and other scrattch functions. In particular, it ensures that columns have a label, an id, and a color, and that there are no factors. It won't overwrite columns that have already been properly process.

Usage

auto_annotate(anno, scale_num = "predicted", na_val_num = 0,
  colorset_num = c("darkblue", "white", "red"), sort_label_cat = TRUE,
  na_val_cat = "ZZ_Missing", colorset_cat = "varibow",
  color_order_cat = "sort")

Arguments

anno	an existing annotation data frame
scale_num	should color scaling of numeric values be "predicted" (default and highly recommended; will return either "linear" or "log10" depending on scaling), "linear","log10","log2", or "zscore".
na_val_num	The value to use to replace NAs for numeric columns. default = 0.
colorset_num	A vector of colors to use for the color gradient. default = c("darkblue","white","red")
sort_label_cat	a logical value to determine if the data in category columns should be arranged alphanumerically before ids are assigned. default = T.
na_val_cat	The value to use to replace NAs in category and factor variables. default = "ZZ_Missing".
colorset_cat	The colorset to use for assigning category and factor colors. Options are "varibow" (default), "rainbow","viridis","inferno","magma", and "terrain"
color_order_cat	The order in which colors should be assigned for cat and factor variables. Options are "sort" and "random". "sort" (default) assigns colors in order; "random" will randomly assign colors.

Value

an updated data frame that has been automatically annotated properly

AllenInstitute/L5_VEN documentation built on July 31, 2022, 6:32 p.m.