In sfisher4/gevitR: minCombinR: Minimal specification syntax for static charts and combinations in R

devtools::load_all() #temporary once things are done
library(dplyr)
library(shiny)

library(treeio)

tree_dat<-input_data(file = system.file("extdata", "sample.nwk", package="treeio"), 
                     dataType = "tree")

genomic_dat<-input_data(file = system.file("extdata", "synth.fasta", package = "mincombinr"),
                        dataType = "dna")

gel_img <- input_data(file = system.file("extdata", "synth_gel_image.tiff", package = "mincombinr"),
                           dataType = "image")


id<-tree_dat@data$tipData

tab_dat<-data.frame(sample_id= id,
                    suscept_status= sample(c("susceptible","resistant"),replace =TRUE,size=length(id)),
                    location = sample(c("School","Community Centre","Hospital"),replace=TRUE,size=length(id)),
                    age = sample(25:80,replace=FALSE,size=length(id)),
                    exposure = sample(c("food","animal","person","unknown"),replace =TRUE,size=length(id)))

sample_date<-c()
sympt_date<-c()
for(i in 1:13){
  tmp<-paste(2017,
        sample(1:12,1),
        sample(1:27,1),sep="-")
  sample_date<-c(sample_date,tmp)
  sympt_date<-c(sympt_date,as.character(as.Date(tmp)+sample(1:50,1)))

}

tab_dat$sample_date<-as.Date(sample_date)
tab_dat$sympt_date<-as.Date(sympt_date)

Some Single Charts

phyloTree_chart <- specify_single(chart_type = "phylogenetic tree", data = "tree_dat")
plot(phyloTree_chart)

timeline_chart <- specify_single(chart_type = "timeline", 
                               data = "tab_dat", 
                               start = "sample_date", 
                               end ="sympt_date", 
                               y = "sample_id")
plot(timeline_chart)

scatter_chart <- specify_single(chart_type = "scatter", data = "tab_dat", x = "sample_id", y = "suscept_status")
plot(scatter_chart)

Combinations

tree_dat_2<-tree_dat
tree_dat_2@data$metadata<-tab_dat

phyloTree_chart_2 <- specify_single(chart_type = "phylogenetic tree", data = "tree_dat_2")

sm_combo_tree <- specify_combination(combo_type = "small_multiple",
                                     base_charts = "phyloTree_chart_2",
                                     facet_by = "exposure")
plot(sm_combo_tree)

composite_combo <- specify_combination(combo_type = "spatial_aligned",
                                       base_charts = c("phyloTree_chart","scatter_chart","timeline_chart"))

plot(composite_combo)

mg_combo <- specify_combination(combo_type = "unaligned",
                                       base_charts = c("phyloTree_chart","scatter_chart","timeline_chart"))

plot(mg_combo)

cl_combo <- specify_combination(combo_type = "color_aligned",
                                       base_charts = c("phyloTree_chart_2","scatter_chart","timeline_chart"),
                                link_by = "exposure")

plot(cl_combo)

gel_img<-annotate_image(gel_img)
tmp<-gel_img@data$metadata #not sure why I had to do this
save(tmp,file="../extdata/syn_gel_image_meta.rds")

load(file="../extdata/syn_gel_image_meta.rds")
meta_img<-inner_join(gel_img@data$metadata,tab_dat,by=c("element_name" = "sample_id"))
gel_img@data$metadata<-meta_img

image_spec<-specify_single(chart_type="image",data="gel_img",color="exposure")
plot(image_spec)

image_spec<-specify_single(chart_type="image",data="gel_img")
scatter_spec<-specify_single(chart_type="scatter",data="tab_dat",x="age",y="location")

color_combo<-specify_combination(combo_type = "color_aligned",base_charts = c("phyloTree_chart_2","timeline_chart","scatter_spec","image_spec"),link_by="exposure")

plot(color_combo)

sfisher4/gevitR documentation built on Feb. 10, 2020, 6:29 p.m.