Swarchal

Swarchal

Swarchal

#!/usr/bin/sh

# script to update R

sudo add-apt-repository "deb http://cran.rstudio.com/bin/linux/ubuntu $(lsb_release -cs)/"
sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9
sudo add-apt-repository -y "ppa:marutter/rrutter"
sudo add-apt-repository -y "ppa:marutter/c2d4u"
sudo apt-get update -qq
sudo apt-get install -y --no-install-recommends r-base-dev r-recommended qpdf

Swarchal

ggplot(data = df_molten,
       aes(x = variable, y = MouseID, fill = value)) + 
    geom_raster() +
    xlab("Protein") + 
    scale_fill_distiller(palette = "RdYlBu", trans = "log10") +         # better colourmap
    theme(axis.text.x = element_text(angle = 90, hjust = 1),
          axis.text.y = element_blank()) + 
    ggtitle("ggplot heatmap") + 
    facet_wrap(~class, scales = "free", ncol = 2)

Swarchal

dat <- df_expression[,2:78]  # numerical columns
rownames(dat) <- df_expression[,1]
row.order <- hclust(dist(dat))$order # clustering
col.order <- hclust(dist(t(dat)))$order
dat_new <- dat[row.order, col.order] # re-order matrix accoring to clustering

df_molten_dat <- melt(as.matrix(dat_new)) # reshape into dataframe
names(df_molten_dat)[c(1:2)] <- c("MouseID", "Protein")

ggplot(data = df_molten_dat,

Swarchal

library(ggplot2)
library(reshape2)

df_expression <- read.csv("expression.csv")
df_molten <- melt(df_expression)
ggplot(data = df_molten,
       aes(x = variable, y = MouseID, fill = value)) + 
    geom_raster() +
    xlab("Protein") + 
    scale_fill_distiller(palette = "RdYlBu", trans = "log10") +

Swarchal

# change colours of channels
plotRGB(image_stack, stretch = 'lin' g = 2, b = 1)

Swarchal

# merge channels
image_stack <- brick(image_DNA, image_actin)

# display merged image
plotRGB(image_stack, stretch = 'lin')

Swarchal

# display images
plot(image_DNA, col = gray.colors(max(values(image_DNA))))
plot(image_actin, col = gray.colors(max(values(image_actin))))