LACE View

The LACE View tool is a visualization application to explore the LACE output.

LACEview depends upon LACE tool, since it is a visualizer for LACE.

LACE installation

Firstly install R (tested on version 4.0)

Inside an R session execute the following commands.

install.packages("devtools", dependencies = TRUE)
install.packages("igraph", dependencies = TRUE)
install.packages("RColorBrewer", dependencies = TRUE)
install.packages("Rfast", dependencies = TRUE)

Now LACE can be installed as follows:

# install CIMLR from Github
library("devtools")
install_github("BIMIB-DISCo/LACE", ref = "master")

# load LACE library
library("LACE")

LACEview Installation

install_github("BIMIB-DISCo/LACEView")

Once both LACE and LACEview are installed. Its time to run the LACE vignette
in the following snippet

library("LACE")
data(longitudinal_sc_variants)
names(longitudinal_sc_variants)
lik_weights = c(0.2308772,0.2554386,0.2701754,0.2435088)
alpha = list()
alpha[[1]] = c(0.02,0.01,0.01,0.01)
alpha[[2]] = c(0.10,0.05,0.05,0.05)
beta = list()
beta[[1]] = c(0.10,0.05,0.05,0.05)
beta[[2]] = c(0.10,0.05,0.05,0.05)
inference = LACE(D = longitudinal_sc_variants, 
    lik_w = lik_weights, 
    alpha = alpha, 
    beta = beta, 
    keep_equivalent = FALSE, 
    num_rs = 5, 
    num_iter = 10, 
    n_try_bs = 5, 
    num_processes = NA, 
    seed = 12345, 
    verbose = FALSE)
clone_labels = c("ARPC2","PRAME","HNRNPC","COL1A2","RPL5","CCT8")

instructions to RUN LACEview

library(LACEview)
LACEview(inference,clone_labels)

The default viewer is too small for LACEview kindly use the enlarged viewer by clicking on the magnifying glass while using Rstudio.

Instructions to Run Other Datasets

The LACE-UTILITIES repo contains two extra datasets with ready made inferences to be plotted using LACEview. [LACE Utils(https://github.com/BIMIB-DISCo/LACE-UTILITIES)

load("~/PATH/TO/INFERENCE/inference.RData")
LACEview(inference,c())