Atwaters/exploreSpectral.Rmd at master · markdane/Atwaters · GitHub

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---
title: "exploreSpectral"
author: "Mark Dane"
date: "January 19, 2016"
output: html_document
---

```{r global_options, include=FALSE}
knitr::opts_chunk$set(fig.width=12, fig.height=8,
                      echo=FALSE, warning=FALSE, message=FALSE)
```

```{r setup}
library("ggplot2")
library("data.table")
library("MEMA")
library("grid")
library("knitr")
library("gplots")
library("RColorBrewer")
library("DT")
library("d3heatmap")
library("plotly")
library(scales)

source("WellPlateFunctions.R")

cDT <- fread("AtwatersCell_v1.0.txt",showProgress=FALSE)
cDT$OmeroDetailURL <- paste0('<a href="https://omero.ohsu.edu/webclient/img_detail/',cDT$ImageID,'/"',' target="_blank">Omero</a>')
cDT$OmeroThumbnailURL <- paste0('<a href="https://omero.ohsu.edu/webclient/render_thumbnail/',cDT$ImageID,'/"',' target="_blank">Omero</a>')
cDT$OmeroImageURL <- paste0('<a href="https://omero.ohsu.edu/webclient/render_image/',cDT$ImageID,'/"',' target="_blank">Omero</a>')
wDT <- fread("AtwatersWell_v1.0.txt")
wDT$OmeroDetailURL <- paste0('<a href="https://omero.ohsu.edu/webclient/img_detail/',wDT$ImageID,'/"',' target="_blank">Omero</a>')
wDT$OmeroThumbnailURL <- paste0('<a href="https://omero.ohsu.edu/webclient/render_thumbnail/',wDT$ImageID,'/"',' target="_blank">Omero</a>')
wDT$OmeroImageURL <- paste0('<a href="https://omero.ohsu.edu/webclient/render_image/',wDT$ImageID,'/"',' target="_blank">Omero</a>')

repDT <- fread("AtwatersRep_v1.0.txt",showProgress=FALSE)
barcodes <- unique(repDT$Barcode)

```


```{r spectral}

DT <- cDT[cDT$GeneSymbol=="NegCtrl"]
DT <- DT[DT$CellLine=="CAL51"]

p <- ggplot(DT, aes(x=log2(MeanIntensityDAPI+1), y=log2(MeanIntensityAlexa488Cyto+1)))+
  geom_point(size=.1)+
  geom_rug(col=rgb(.5,0,0,alpha=.01))+
  ggtitle("KRT5 vs. Mean DAPI in NegCtrl")+
  facet_wrap(~Well,scales = "free_y",labeller = labeller(Plate = label_both, CellLine = label_value))
print(p)

p <- ggplot(DT, aes(x=log2(MeanIntensityAlexa488Cyto+1), y=log2(MeanIntensityAlexa555Cyto+1)))+
  geom_point(size=.1)+
  geom_rug(col=rgb(.5,0,0,alpha=.01))+
  ggtitle("KRT19 vs. KRT5 in NegCtrl")+
  coord_cartesian(xlim=c(4,11),ylim=c(4,11))+
  facet_wrap(~Well,scales = "free_y",labeller = labeller(Plate = label_both, CellLine = label_value))
print(p)

p <- ggplot(DT, aes(x=log2(MeanIntensityAlexa555Cyto+1), y=log2(MeanIntensityAlexa647+1)))+
  geom_point(size=.1)+
  geom_rug(col=rgb(.5,0,0,alpha=.01))+
  ggtitle("EdU vs. KRT19 in NegCtrl")+
  facet_wrap(~Well,scales = "free_y",labeller = labeller(Plate = label_both, CellLine = label_value))
print(p)

```