kidney_wt/ko

{r setup, include=FALSE} knitr::opts_chunk$set(echo = TRUE)

library(rsconnect)
library(Biobase)
library(SafeQuant)
library(Ringo)
library(dplyr)
library(ggplot2)

ko_wt<- `Phospho.(STY)Sites`

#View(ko_wt)

ko_wt$Positions.within.proteins <- NULL

#cols.dont.want <- c("Leading.proteins", "Protein", 'Fasta.headers', 'Localization.prob','Score.diff','PEP','Delta.score','Score.for.localization')

#ko_wt <- ko_wt[, ! names(ko_wt) %in% cols.dont.want, drop = F]

columnsYES <- as.vector(c('Proteins','Score','Localization.prob.KO','Localization.prob.WT', 'Number.of.Phospho..STY.','Amino.acid','Charge','Intensity','Reverse','Potential.contaminant','Protein.group.IDs'))

ko_wt <- ko_wt[ ,columnsYES]
ko_wt

#columnsYES

filterdScore <- filter(ko_wt,
       Score > 40)

filterdScore [ ! filterdScore$Reverse %in% '+', ]
filterdScore [ ! filterdScore$Potential.contaminant %in% '+', ]

plot(row.names(filterdScore), filterdScore$Localization.prob.WT)

tfs<- sqrt(filterdScore$Intensity)

qqnorm(filterdScore$Intensity )
qqnorm(tfs)
qqplot( filterdScore$Intensity,tfs)

library(readxl)
PS <- read_excel("N:/TSever/20181218_vsaka_frakcija_scx_posebaj_kidney_ko+wt/combined/txt/Phospho (STY)Sites.xlsx")
#View(PS)

library(readr)
Phospho_STY_Sites <- read_delim("N:/TSever/20181218_vsaka_frakcija_scx_posebaj_kidney_ko+wt/combined/txt/Phospho (STY)Sites.txt", 
    "\t", escape_double = FALSE, trim_ws = TRUE)
#View(Phospho_STY_Sites)

KO_005 <-rowMeans(Phospho_STY_Sites[c('Intensity KO_005' )])

ggplot(Phospho_STY_Sites, aes(Phospho_STY_Sites$`Intensity WT_000`)) +
  geom_histogram()

a <- data.frame(intensity = c(0,    0,  192040, 0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  348255787,  0,  0,  0,  0,  0,  715160, 0,  0,  5337080,    0,  0,  0,  0,  0))

a[,2]<- c('Intensity KO_005',   'Intensity KO_010', 'Intensity KO_015', 'Intensity KO_020', 'Intensity KO_025', 'Intensity KO_030', 'Intensity KO_035', 'Intensity KO_040', 'Intensity KO_045', 'Intensity KO_050','Intensity KO_060',  'Intensity KO_070', 'Intensity KO_080', 'Intensity KO_090', 'Intensity KO_100', 'Intensity WT_000', 'Intensity Wt_010', 'Intensity WT_015', 'Intensity WT_020', 'Intensity WT_025', 'Intensity WT_030', 'Intensity WT_035', 'Intensity WT_040', 'Intensity WT_045', 'Intensity WT_050', 'Intensity WT_060', 'Intensity WT_070', 'Intensity WT_080', 'Intensity WT_090', 'Intensity WT_100')

Phospho_STY_Sites2<- filter(Phospho_STY_Sites,
       Score > 40)
Phospho_STY_Sites2<- filter(Phospho_STY_Sites2,
                            `Localization prob` > 0.75)

Phospho_STY_Sites2 [ ! Phospho_STY_Sites2$Reverse %in% '+', ]
Phospho_STY_Sites2 [ ! Phospho_STY_Sites2$`Potential contaminant` %in% '+', ]

wt000<-
  ggplot(Phospho_STY_Sites2, aes(`Intensity WT_000`, 1:length(Score))) +
  geom_point(color='#77b800', size=2)+
  labs(y='Leading protein')+
  scale_y_continuous(breaks=c(1:88),
  labels=c(Phospho_STY_Sites2$`Leading proteins`))+
  coord_flip()+
  theme_minimal()+
  theme(axis.text.x=element_text(angle=80, hjust=1))

plot(Phospho_STY_Sites2$`Intensity WT_000`, 1:88)

wt050<-
  ggplot(Phospho_STY_Sites2, aes(`Intensity WT_050`, 1:length(Score))) +
  geom_point(color='#77b800')+
  labs(y='Leading protein')+
  scale_y_continuous(breaks=c(1:length(Phospho_STY_Sites2$`Leading proteins`)),
  labels=c(Phospho_STY_Sites2$`Leading proteins`))+
  coord_flip()+
  theme_minimal()+
  theme(axis.text.x=element_text(angle=80, hjust=1))

wt010<-
  ggplot(Phospho_STY_Sites2, aes(`Intensity WT_010`, 1:length(Score))) +
  geom_point(color='#77b800', size=2)+
  labs(y='Leading protein')+
  scale_y_continuous(breaks=c(1:length(Phospho_STY_Sites2$`Leading proteins`)),
  labels=c(Phospho_STY_Sites2$`Leading proteins`))+
  coord_flip()+
  theme_minimal()+
  theme(axis.text.x=element_text(angle=80, hjust=1))

wt015<-
  ggplot(Phospho_STY_Sites2, aes(`Intensity WT_015`, 1:length(Score))) +
  geom_point(color='#77b800', size=2)+
  labs(y='Leading protein')+
  scale_y_continuous(breaks=c(1:length(Phospho_STY_Sites2$`Leading proteins`)),
  labels=c(Phospho_STY_Sites2$`Leading proteins`))+
  coord_flip()+
  theme_minimal()+
  theme(axis.text.x=element_text(angle=80, hjust=1))

wt_unique<-c(
length(unique(c(Phospho_STY_Sites2$`Intensity WT_000`))),
1,
length(unique(c(Phospho_STY_Sites2$`Intensity Wt_010`))),
length(unique(c(Phospho_STY_Sites2$`Intensity WT_015`))),
length(unique(c(Phospho_STY_Sites2$`Intensity WT_020`))),
length(unique(c(Phospho_STY_Sites2$`Intensity WT_025`))),
length(unique(c(Phospho_STY_Sites2$`Intensity WT_030`))),
length(unique(c(Phospho_STY_Sites2$`Intensity WT_035`))),
length(unique(c(Phospho_STY_Sites2$`Intensity WT_040`))),
length(unique(c(Phospho_STY_Sites2$`Intensity WT_045`))),
length(unique(c(Phospho_STY_Sites2$`Intensity WT_050`))),
length(unique(c(Phospho_STY_Sites2$`Intensity WT_060`))),
length(unique(c(Phospho_STY_Sites2$`Intensity WT_070`))),
length(unique(c(Phospho_STY_Sites2$`Intensity WT_080`))),
length(unique(c(Phospho_STY_Sites2$`Intensity WT_090`))),
length(unique(c(Phospho_STY_Sites2$`Intensity WT_100`)))
)-1

ko_unique<-c(
1,  
length(unique(c(Phospho_STY_Sites2$`Intensity KO_005`))),
length(unique(c(Phospho_STY_Sites2$`Intensity KO_010`))),
length(unique(c(Phospho_STY_Sites2$`Intensity WT_015`))),
length(unique(c(Phospho_STY_Sites2$`Intensity WT_020`))),
length(unique(c(Phospho_STY_Sites2$`Intensity WT_025`))),
length(unique(c(Phospho_STY_Sites2$`Intensity WT_030`))),
length(unique(c(Phospho_STY_Sites2$`Intensity WT_035`))),
length(unique(c(Phospho_STY_Sites2$`Intensity WT_040`))),
length(unique(c(Phospho_STY_Sites2$`Intensity WT_045`))),
length(unique(c(Phospho_STY_Sites2$`Intensity WT_050`))),
length(unique(c(Phospho_STY_Sites2$`Intensity WT_060`))),
length(unique(c(Phospho_STY_Sites2$`Intensity WT_070`))),
length(unique(c(Phospho_STY_Sites2$`Intensity WT_080`))),
length(unique(c(Phospho_STY_Sites2$`Intensity WT_090`))),
length(unique(c(Phospho_STY_Sites2$`Intensity WT_100`)))
)-1

ggplot()+
  geom_bar(stat='identity',
           aes(1:length(wt_unique),wt_unique), fill='#00cfcf', alpha=0.5, size=1.5)+
  
  geom_bar(stat='identity',
             aes(1:length(wt_unique),ko_unique), fill='#cf0000', alpha=0.5, size=1.5)+
  theme_light()+
  scale_x_continuous(breaks = c(1:length(ko_unique)),
    labels=c('0 M','0.05 M','0.10 M','0.15 M', '0.20 M', '0.25 M', '0.30 M', '0.35 M', '0.40 M', '0.45 M', '0.50 M', '0.60 M', '0.70 M',        '0.80 M', '0.90 M',' 1 M' ))+
  labs(x='NaCl fraction', y='number of proteins')+
  theme(legend.position = 'right')+
  ggtitle('number of phophoprylated protein in each scx fraction')+
  ylim(0,90)+
  theme(plot.title = element_text(hjust=0.5))+
  geom_rect(aes(xmin=13, xmax=16, ymin=60,ymax=83),color='#000000', fill='#ffffff', alpha=1)+
  geom_rect(aes(xmin=13.5, xmax=14, ymin=63,ymax=66),color='#000000', fill='#00cfcf', alpha=0.5)+
  geom_rect(aes(xmin=13.5, xmax=14, ymin=70,ymax=73),color='#000000', fill='#cf0000', alpha=0.5)+
  geom_rect(aes(xmin=13.5, xmax=14, ymin=77,ymax=80),color='#000000', fill='#844B4B', alpha=0.5)+
  annotate("text", x = 15, y = 65, label = "WT",color='#000000')+
  annotate("text", x = 15, y = 72, label = "KO",color='#000000')+
  annotate("text", x = 15, y = 79, label = "overlap",color='#000000')+
  theme(axis.text.x=element_text(angle=45, hjust=1))

kidney_wt/ko_phospho