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Merge pull request #22 from msk-access/feature/plot_fix
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Feature/plot fix
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@rhshah
rhshah authored Jul 21, 2020
2 parents 641224e + 7241c34 commit a8e41c3
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Showing 2 changed files with 56 additions and 34 deletions.
2 changes: 1 addition & 1 deletion R/filter_calls.R
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Original file line number Diff line number Diff line change
Expand Up @@ -39,7 +39,7 @@ filter_calls = function(

# for each patient produce the correct results ----------------------------
# x <- unique(master.ref$cmo_patient_id)[1]
all.fillout.dim <- lapply(unique(master.ref[cmo_patient_id == 'C-DFJ7RT']$cmo_patient_id),function(x){
all.fillout.dim <- lapply(unique(master.ref$cmo_patient_id),function(x){
print(paste0('Processing patient ',x))
# Inputs and sanity checks ------------------------------------------------
fillouts.filenames <- list.files(paste0(results.dir,'/',x,'/'),'ORG-STD_genotyped.maf|ORG-SIMPLEX-DUPLEX_genotyped.maf',full.names = T)
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88 changes: 55 additions & 33 deletions R/plot_all_events.R
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Original file line number Diff line number Diff line change
Expand Up @@ -194,48 +194,70 @@ plot_all_events <- function(
tmp.cna <- do.call(rbind, lapply(master.ref[cmo_patient_id == x]$cmo_sample_id_plasma, function(y) {
fread(paste0(results.dir, "/CNA_final_call_set/", y, "_cna_final_call_set.txt"))
}))


transform.vector = structure(as.numeric(master.ref[cmo_patient_id == x]$collection_date),
names = master.ref[cmo_patient_id == x]$cmo_sample_id_plasma)
print(transform.vector)
tmp.table$Tumor_Sample_Barcode = factor(transform.vector[tmp.table$Tumor_Sample_Barcode], levels = sort(transform.vector))

if(nrow(tmp.table) == 0 | all(tmp.table$t_alt_count == 0)){
print('skiping to the next')
if(nrow(tmp.cna)) stop(paste0('Need to make CNA only file for: ',x))
if (all(!is.na(as.Date(master.ref[cmo_patient_id == x]$collection_date, "%m/%d/%y")))) {
transform.vector <- structure(as.Date(master.ref[cmo_patient_id == x]$collection_date, "%m/%d/%y"),
names = master.ref[cmo_patient_id == x]$cmo_sample_id_plasma
)
print("###Date Presentation:####")
print(transform.vector)
}
else {
transform.vector <- structure(as.character(master.ref[cmo_patient_id == x]$collection_date),
names = master.ref[cmo_patient_id == x]$cmo_sample_id_plasma
)
print(transform.vector)
}
tmp.table$Tumor_Sample_Barcode <- transform.vector[tmp.table$Tumor_Sample_Barcode]
print(tmp.table)
if (nrow(tmp.table) == 0 | all(tmp.table$t_alt_count == 0)) {
print("skiping to the next")
if (nrow(tmp.cna)) stop(paste0("Need to make CNA only file for: ", x))
return()
}

colourCount = nrow(unique(tmp.table[,.(Hugo_Symbol,HGVSp_Short)]))
getPalette = colorRampPalette(brewer.pal(8, "Set2"))
SNV.SV.plot = ggplot(tmp.table) +
geom_line(aes(x = Tumor_Sample_Barcode, y = ifelse(t_total_count == 0, 0, as.numeric(t_alt_count/t_total_count)),
color = paste0(Hugo_Symbol,' ',ifelse(grepl('^p\\.',HGVSp_Short),HGVSp_Short,'')),group = paste0(Hugo_Symbol,'_',HGVSp_Short))) +
geom_point(aes(x = Tumor_Sample_Barcode, y = ifelse(t_total_count == 0, 0, as.numeric(t_alt_count/t_total_count)),
color = paste0(Hugo_Symbol,' ',ifelse(grepl('^p\\.',HGVSp_Short),HGVSp_Short,'')),shape = call_confidence),size = 1.5) +
labs(title=x,x='Time Point', y='VAF') +
scale_shape_manual(values=status_id,name = 'Call Status') + scale_color_manual(values = getPalette(colourCount),name = 'Alteration') +
theme_minimal() + scale_y_log10() +
theme(panel.grid.major = element_blank(),legend.position="top",legend.box = "vertical",
axis.text.x = element_text(angle=45, hjust=1, face = 'bold'))

colourCount <- nrow(unique(tmp.table[, .(Hugo_Symbol, HGVSp_Short)]))
getPalette <- colorRampPalette(brewer.pal(8, "Set2"))
SNV.SV.plot <- ggplot(tmp.table) +
geom_line(aes(
x = Tumor_Sample_Barcode, y = ifelse(t_total_count == 0, 0, as.numeric(t_alt_count / t_total_count)),
color = paste0(Hugo_Symbol, " ", ifelse(grepl("^p\\.", HGVSp_Short), HGVSp_Short, "")), group = paste0(Hugo_Symbol, "_", HGVSp_Short)
)) +
geom_point(aes(
x = Tumor_Sample_Barcode, y = ifelse(t_total_count == 0, 0, as.numeric(t_alt_count / t_total_count)),
color = paste0(Hugo_Symbol, " ", ifelse(grepl("^p\\.", HGVSp_Short), HGVSp_Short, "")), shape = call_confidence
), size = 1.5) +
labs(title = x, x = "Time Point", y = "VAF") +
scale_shape_manual(values = status_id, name = "Call Status") +
scale_color_manual(values = getPalette(colourCount), name = "Alteration") +
theme_minimal() +
scale_y_log10() +
scale_x_date(date_minor_breaks = "1 day", date_breaks = "1 week", date_labels = "%b %d") +
theme(
panel.grid.major = element_blank(), legend.position = "top", legend.box = "vertical",
axis.text.x = element_text(angle = 45, hjust = 1, face = "bold")
)
print(SNV.SV.plot)

if (nrow(tmp.cna) > 0) {
tmp.cna <- tmp.cna %>%
mutate(Tumor_Sample_Barcode = factor(Tumor_Sample_Barcode, unique(tmp.sample.sheets[Sample_Type == "duplex"]$Sample_Barcode))) %>%
# expand table on all empty samples without any calls
data.table() %>% dcast.data.table(Hugo_Symbol + CNA ~ Tumor_Sample_Barcode,drop = c(TRUE, FALSE),fill = 0,value.var = 'fc') %>%
melt.data.table(id.vars = c('Hugo_Symbol','CNA'),variable.name = 'Tumor_Sample_Barcode',value.name = 'fc') %>% data.table()
tmp.cna$Tumor_Sample_Barcode = transform.vector[tmp.cna$Tumor_Sample_Barcode]

colourCount = nrow(unique(tmp.cna[,.(Hugo_Symbol,CNA)]))
getPalette = colorRampPalette(brewer.pal(8, "Set2"))
CNA.plot = ggplot(tmp.cna) +
geom_bar(aes(x = Tumor_Sample_Barcode,y = abs(fc),fill = paste0(Hugo_Symbol,'_',CNA)),position="dodge", stat="identity") +
labs(x='Time Point', y='Absolute fc') +
scale_fill_manual(values = getPalette(colourCount),name = 'Alteration') +
theme_minimal() + theme(panel.grid.major = element_blank(),legend.position="bottom",axis.text.x = element_text(angle=45, hjust=1,face = 'bold'))
data.table() %>%
dcast.data.table(Hugo_Symbol + CNA ~ Tumor_Sample_Barcode, drop = c(TRUE, FALSE), fill = 0, value.var = "fc") %>%
melt.data.table(id.vars = c("Hugo_Symbol", "CNA"), variable.name = "Tumor_Sample_Barcode", value.name = "fc") %>%
data.table()
tmp.cna$Tumor_Sample_Barcode <- transform.vector[tmp.cna$Tumor_Sample_Barcode]

colourCount <- nrow(unique(tmp.cna[, .(Hugo_Symbol, CNA)]))
getPalette <- colorRampPalette(brewer.pal(8, "Set2"))
CNA.plot <- ggplot(tmp.cna) +
geom_bar(aes(x = Tumor_Sample_Barcode, y = abs(fc), fill = paste0(Hugo_Symbol, "_", CNA)), position = "dodge", stat = "identity") +
labs(x = "Time Point", y = "Absolute fc") +
scale_fill_manual(values = getPalette(colourCount), name = "Alteration") +
theme_minimal() +
scale_x_date(date_minor_breaks = "1 day", date_breaks = "1 week", date_labels = "%b %d") +
theme(panel.grid.major = element_blank(), legend.position = "bottom", axis.text.x = element_text(angle = 45, hjust = 1, face = "bold"))
print(CNA.plot)

pdf(paste0(output.dir, "/", x, "_all_events.pdf"), width = 10, height = 7)
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