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@davidebolo1993
davidebolo1993 committed Apr 17, 2023
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2 changes: 1 addition & 1 deletion .Rproj.user/F43DE67C/pcs/files-pane.pper
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2 changes: 1 addition & 1 deletion .Rproj.user/F43DE67C/pcs/source-pane.pper
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12 changes: 6 additions & 6 deletions .Rproj.user/F43DE67C/pcs/windowlayoutstate.pper
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3 changes: 3 additions & 0 deletions .Rproj.user/F43DE67C/sources/prop/INDEX
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~%2FNanoR%2FDESCRIPTION="300FBE73"
~%2FNanoR%2FR%2Fcompare.R="DDB686B2"
~%2FNanoR%2FR%2Fmuxscan.R="68F33D03"
~%2FNanoR%2FREADME.md="668CEBF6"
~%2FNanoR%2Fman%2Fcompare.Rd="35EB6A46"
40 changes: 27 additions & 13 deletions R/compare.R
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@@ -1,6 +1,7 @@
#' @title compare
#' @description generate an interactive HTML report comparing length and quality of reads from multiple sequencing summary files
#' @param summaries a character vector containing paths to multiple sequencing summaries (each from a different ONT sequencing run)
#' @param labels a character vector containing ordered names for the sequencing files. Override the default behaviour, which is to use the run_id
#' @param time compare run statistics using this time interval (hours). Default to 10
#' @param out path to HTML report
#' @return HTML file
Expand All @@ -9,10 +10,10 @@
#' exp1<-file.path("/path/to/exp1_sequencing_summary.txt")
#' exp2<-file.path("/path/to/exp2_sequencing_summary.txt")
#' outhtml<-file.path("/path/to/comparison.html")
#' NanoR::compare(summaries=c(exp1,exp2), fraction=.001, out=outhtml)
#' NanoR::compare(summaries=c(exp1,exp2), time=10, out=outhtml)


compare<-function(summaries,time=10,out){
compare<-function(summaries,labels=NULL,time=10,out){


out<-file.path(out)
Expand All @@ -24,23 +25,36 @@ compare<-function(summaries,time=10,out){
for (i in c(1:(length(compare_)-1))) {

h<-seq(from=compare_[i], to=compare_[i+1], by=1)

for (n in h) {

clist[[as.character(n)]]<-paste(h[1], h[length(h)],sep="-")

}
}


if (!is.null(labels)) {

if (length(labels) != length(summaries)) {

stop("[",Sys.time(),"]"," length of summaries and labels vector must be the same")

}

}

l<-1

for (summary in summaries) {

summary<-normalizePath(file.path(summary))

message("[",Sys.time(),"]"," reading sequencing summary file ", summary)

tab<-fread(summary,sep="\t",header=TRUE,showProgress=FALSE)
run<-unique(tab$run_id)
run<-ifelse(is.null(labels), unique(tab$run_id),labels[l])
l<-l+1

if (length(run) != 1) {

Expand All @@ -67,7 +81,7 @@ compare<-function(summaries,time=10,out){
range_<-clist[[as.character(from)]]

summ[i,]$x<-summ_pass[i,]$x<-range_

summ[i,]$y<-nrow(subtab)
summ_pass[i,]$y<-nrow(subset(subtab, (subtab$passes_filtering == TRUE)))

Expand All @@ -91,7 +105,7 @@ compare<-function(summaries,time=10,out){
taball_pass[[run]]<-summ_pass

}

taball<-do.call(rbind, taball)
taball_pass<-do.call(rbind,taball_pass)

Expand Down Expand Up @@ -124,22 +138,22 @@ compare<-function(summaries,time=10,out){


p1 <- plot_ly() %>% add_trace(x = taball$x, y = taball$y, color = taball$z, type = "box", visible=TRUE,legendgroup = taball$z,showlegend=F) %>%
add_trace(x=taball_pass$x,y=taball_pass$y,color = taball_pass$z, type = "box", visible=FALSE,legendgroup = taball_pass$z,showlegend=F) %>%
layout(boxmode = "group",legend = list(orientation = 'h'),updatemenus = list(chart_type), xaxis=list(title="Sequencing run-time (h)",titlefont=f,tickangle=45),
add_trace(x=taball_pass$x,y=taball_pass$y,color = taball_pass$z, type = "box", visible=FALSE,legendgroup = taball_pass$z,showlegend=F) %>%
layout(boxmode = "group",legend = list(orientation = 'h'),updatemenus = list(chart_type), xaxis=list(title="Sequencing run-time (h)",titlefont=f,tickangle=45),
yaxis=list(side="left",title="#reads",titlefont=f))

p2 <- plot_ly() %>% add_trace(x = taball$x, y = taball$y2, color = taball$z, type = "box", visible=TRUE,legendgroup = taball$z,showlegend=F) %>%
add_trace(x=taball_pass$x,y=taball_pass$y2,color = taball_pass$z, type = "box", visible=FALSE,legendgroup=taball_pass$z,showlegend=F) %>%
add_trace(x=taball_pass$x,y=taball_pass$y2,color = taball_pass$z, type = "box", visible=FALSE,legendgroup=taball_pass$z,showlegend=F) %>%
layout(boxmode = "group",legend = list(orientation = 'h'),updatemenus = list(chart_type), xaxis=list(title="Sequencing run-time (h)",titlefont=f,tickangle=45),
yaxis=list(side="left",title="#bases",titlefont=f))

p3 <- plot_ly() %>% add_trace(x = taball$x, y = taball$y3, color = taball$z, type = "box", visible=TRUE,legendgroup = taball$z,showlegend=F) %>%
add_trace(x=taball_pass$x,y=taball_pass$y3,color = taball_pass$z, type = "box", visible=FALSE,legendgroup=taball_pass$z,showlegend=F) %>%
add_trace(x=taball_pass$x,y=taball_pass$y3,color = taball_pass$z, type = "box", visible=FALSE,legendgroup=taball_pass$z,showlegend=F) %>%
layout(boxmode = "group",legend = list(orientation = 'h'),updatemenus = list(chart_type), xaxis=list(title="Sequencing run-time (h)",titlefont=f,tickangle=45),
yaxis=list(side="left",title="Length",titlefont=f))

p4<- plot_ly() %>% add_trace(x = taball$x, y = taball$y4, color = taball$z, type = "box", visible=TRUE,legendgroup = taball$z) %>%
add_trace(x=taball_pass$x,y=taball_pass$y4,color = taball_pass$z, type = "box", visible=FALSE, legendgroup=taball_pass$z) %>%
add_trace(x=taball_pass$x,y=taball_pass$y4,color = taball_pass$z, type = "box", visible=FALSE, legendgroup=taball_pass$z) %>%
layout(boxmode = "group",legend = list(orientation = 'h'),updatemenus = list(chart_type), xaxis=list(title="Sequencing run-time (h)",titlefont=f,tickangle=45),
yaxis=list(side="left",title="Qscore",titlefont=f))

Expand All @@ -157,4 +171,4 @@ compare<-function(summaries,time=10,out){
message("[",Sys.time(),"]"," done")


}
}
6 changes: 4 additions & 2 deletions man/compare.Rd
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