[feat] update R source

Author: progistar

figR/ExtFig10.R

@@ -1,11 +1,11 @@
 library(networkD3)
 library(htmlwidgets)
 
-########## ExtFig. 10: Reannotation of previously reported cis- and trans-spliced pMHC-I peptides ##########
+########## ExtFig. 10: Reannotation of previously reported cis- and trans-spliced pMHC-I sequences ##########
 ## deconvolution of locations
 # after removing values below cutoff
 # run annotate function in PepQueryMHC
-annotations <- read_excel("SupplementaryTable5.xlsx", sheet = "C1R_Top_annotation")
+annotations <- read_excel("SupplementaryTable5.xlsx", sheet = "Top annotation")
 
 # drop null
 annotations <- annotations[annotations$Comparison != "Not found", ]

figR/ExtFig7,8.R

@@ -11,7 +11,7 @@ source("Color.R")
 
 ########## ExtFig. 7,8: Overall expression across the tumor antigens ##########
 tumor_antigens <- read_excel(path = "SupplementaryTable3.xlsx", sheet = "final tumor antigens (PQM)")
-cutoff_1p <-read_excel(path = "SupplementaryTable3.xlsx", sheet = "p-value cutoff (log2(RPHM+1))")
+cutoff_1p <-read_excel(path = "SupplementaryTable3.xlsx", sheet = "cutoff (log2(RPHM+1))")
 
 
 ### Extend version

figR/Fig2a.R

@@ -10,7 +10,6 @@ source("Color.R")
 
 pepquerymhc_tumor_antigens <- read_excel(path = "SupplementaryTable3.xlsx", sheet = "final tumor antigens (PQM)")
 bamquery_tumor_antigens <- read_excel(path = "SupplementaryTable3.xlsx", sheet = "final tumor antigens (BQ)")
-cutoff_1p <-read_excel(path = "SupplementaryTable3.xlsx", sheet = "p-value cutoff (log2(RPHM+1))")
 
 ########## Fig. 2a: Tumor antigen heatmap ##########
 dev.off()

figR/Fig2d,e.R

@@ -9,7 +9,7 @@ library(tidyr)
 source("Color.R")
 
 ########## Fig. 2d: Proportion of type ##########
-annotations <- read_excel("SupplementaryTable5.xlsx", sheet = "C1R_Top_annotation")
+annotations <- read_excel("SupplementaryTable5.xlsx", sheet = "Top annotation")
 
 annotations$Category <- "Reference"
 annotations[annotations$`PepQueryMHC:Unique_class_code` != "PC", ]$Category <- "Non-reference"
@@ -55,7 +55,7 @@ ggsave(filename = "Fig2d.png", plot = plot_time_top, height = 7, width = 1.8, dp
 ########## Fig.2e: RPHM value per each peptide ##########
 pepquerymhc <- read_excel("SupplementaryTable5.xlsx", sheet = "PepQueryMHC")
 bamquery <- read_excel("SupplementaryTable5.xlsx", sheet = "BamQuery")
-cutoffs <- read_excel("SupplementaryTable3.xlsx", sheet = "p-value cutoff (log2(RPHM+1))")
+cutoffs <- read_excel("SupplementaryTable3.xlsx", sheet = "cutoff (log2(RPHM+1))")
 input_data <- read_excel("SupplementaryTable1.xlsx", sheet = "Spliced-MHC-I")
 names(input_data)[names(input_data) == 'Sequence'] <- "DeNovoSequence"