Scott Warchal Swarchal
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| source_https <- function(url, ...) { | |
| # load package | |
| require(RCurl) | |
| # parse and evaluate each .R script | |
| sapply(c(url, ...), function(u) { | |
| eval( | |
| parse( | |
| text = getURL(u, followlocation = TRUE, | |
| cainfo = system.file("CurlSSL", |
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| path <- paste(getwd(), "\\", sep = "") | |
| files <- list.files(path=path, pattern="*.csv") | |
| for(file in files) | |
| { | |
| perpos <- which(strsplit(file, "")[[1]]==".") | |
| assign( | |
| gsub(" ","",substr(file, 1, perpos-1)), | |
| read.csv(paste(path,file,sep=""))) | |
| } |
Swarchal
/ sliding_histogram_wally.py
Last active
November 9, 2015 21:13
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| import matplotlib.pyplot as plt | |
| from skimage.io import imread | |
| from skimage.morphology import disk | |
| from skimage.filters import rank | |
| import numpy as np | |
| im_all = imread("/home/scott/Dropbox/wally/ww2.jpg") | |
| all_red = im_all[:, :, 0] | |
| im_wally = imread("/home/scott/Dropbox/wally/wally2.png") | |
| wally_red = im_wally[:, :, 0] |
Swarchal
/ template_match.py
Created
November 9, 2015 21:23
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| import matplotlib.pyplot as plt | |
| from skimage.io import imread | |
| from skimage.feature import match_template | |
| import matplotlib.pyplot as plt | |
| import numpy as np | |
| image = imread("image.jpg") | |
| wally = imread("wally.png") | |
| # select just the red channel |
Swarchal
/ open_files.R
Created
November 12, 2015 20:39
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| library(raster) | |
| # load images | |
| image_DNA <- raster('~/BBBC007_v1_images/A9/A9 p5d.tif') | |
| image_actin <- raster('~/BBBC007_v1_images/A9/A9 p5f.tif') |
Swarchal
/ display_images.R
Created
November 12, 2015 20:40
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| # display images | |
| plot(image_DNA, col = gray.colors(max(values(image_DNA)))) | |
| plot(image_actin, col = gray.colors(max(values(image_actin)))) |
Swarchal
/ merge_and_display.R
Created
November 12, 2015 20:41
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| # merge channels | |
| image_stack <- brick(image_DNA, image_actin) | |
| # display merged image | |
| plotRGB(image_stack, stretch = 'lin') |
Swarchal
/ change_colours.R
Created
November 12, 2015 20:42
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| # change colours of channels | |
| plotRGB(image_stack, stretch = 'lin' g = 2, b = 1) |
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| 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
/ heatmap_clustered.R
Last active
November 25, 2015 01:12
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| 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, |
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