# Load packages
library(GAMBLR.open)
library(tidyverse)
Tutorial: Getting started
This is a quick tour of some basic commands and usage patterns, just to get you started.
This tutorial explores how to generate some basic and most common plots, commonly occurring arguments across different functions, best practices and recommendations in the scope of visualizing data.
What are standartized colours?
First, let’s explore the standartized color pallettes in the GAMBLR.viz. They are stored as list in one of the GAMBLR.viz dependencies (GAMBLR.helpers) and are an integral part of visualizations. For demonstration purposes, we will obtain all of the standartized colours:
<- get_gambl_colours(
all_c as_dataframe = TRUE
)
What are the colours available?
str(all_c)
'data.frame': 328 obs. of 3 variables:
$ group : chr "chromosome" "chromosome" "chromosome" "chromosome" ...
$ name : chr "chr1" "chr2" "chr3" "chr4" ...
$ colour: chr "#555FAB" "#CE3D31" "#749B58" "#F0E584" ...
What are the colour groups?
table(all_c$group)
aneuploidy BL blood chapuy_classifier
8 7 15 6
chromosome clinical cohort coo
23 47 16 12
copy_number domains EBV FL
17 24 4 3
genetic_subgroup hmrn indels lacy_classifier
24 8 2 8
lymphgen lymphgenerator mutation pathology
14 10 15 32
pos_neg rainfall seq_type sex
13 7 3 6
svs type
2 2
Many of these colours are conviniently provided for you to ensure consistency that is independent of formatting and case: for example, when the color for DLBCL COO is returned, the same color will be used for UNCLASS
, U
, UNC
, Unclassified
etc.
Just for the purpose of this guide, we will define a simple function to display some of these colour pallettes:
<- function(data, group){
show_col %>%
data filter(
!!sym("group") == {{group}}
%>%
) ggplot(
aes(
x = name,
y = 0,
fill = colour,
label = name
)+
) geom_tile(width = 0.9, height = 1) +
geom_text(color = "white", fontface="bold") +
scale_fill_identity(guide = "none") +
coord_flip() +
theme_void() +
labs(title = toupper(group)) +
theme(plot.title = element_text(lineheight = 0.9,hjust=0.5,face="bold"))
}
Hex codes for B-cell lymphomas
show_col(all_c, "pathology")
Hex codes for genetic subgroups
show_col(all_c, "genetic_subgroup")
Hex codes for clinical variables
show_col(all_c, "clinical")
Hex codes for Mutation types
show_col(all_c, "mutation")