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Citations since 2017
102 Research Items
Afshin Beheshti currently works at KBR at NASA Ames Research Center. Afshin does research in space biology, COVID-19, radiation biology, and Cancer Research. His current projects include is 'Omics for Space Biology: The GeneLab project', miRNA impact on cancer, and COVID-19.
March 2020 - present
COVID-19 International Research Team
- I'm a Co-lead of a non-profit called COVID-19 International Research Team (COV-IRT, www.cov-irt.org), comprising of scientists driving research into COVID-19. This interdisciplinary group from over 70 institutions worldwide is coordinating projects focused specifically on SARS-CoV-2, including determining heterogeneity of the viral genome sequence, analyzing host response to COVID-19 disease, characterizing potential co-infections, and identifying potential therapeutic targets.
I'm fairly in new with R, so any help is much appreciated. I'm in the process of making a heatmap using the pheatmap function. I'm adding a column color bar so that I can associate specific data in the header with specific colors in the color bar. So for example I want anything that contains the number 1 in the header of my entire data set to be labeled as Male and have a specific color associated with it in the column color bar.
I'm using the following code as an example to try to do this:
# dummy data
dummymat = matrix(rnorm(100), 10, 10)
colnames(dummymat) = paste("Patient", 1:10, sep = "")
rownames(dummymat) = paste("Gene", 1:10, sep = "")
# create a data frame with the patients categories
categories <- data.frame(Sex = factor(sample(c("1", "2"),size = 10,replace = T), labels = c("Male", "Female")), Stage= factor(sample(c('Patient10','Patient9','patient5'),size = 10,replace = T), labels = c('I','II','III')))
rownames(categories) <- colnames(dummymat)
pheatmap(dummymat, color = colorRampPalette(c("navy", "white", "firebrick3"))(50), clustering_method = "mcquitty",
clustering_distance_rows = "euclidean", clustering_distance_cols = "euclidean", scale = 'none', annotation = categories)
Obviously from the above code I don't get what I want. I'm sure I using the wrong functions here to do this (since I'm a beginner in R)
Can anyone help with my question? I would really appreciate any input and help that anyone can give.
The multi-year GeneLab project is both a science collaboration initiative as well as a data system effort providing a collaborative workspace with tools to analyze and visualize space relevant omics data. Our mission is to maximize the utilization of the valuable biological research resources aboard the International Space Station (ISS) by collecting genomic, transcriptomic, proteomic, and metabolomics data known as “omics”. One important aspect of GeneLab’s mission is to help the scientific community and the population at large gain new knowledge from space omics data. By providing a portal linking processed data to flight parameters, GeneLab enables exploration of the molecular network responses of terrestrial biology to the space environment, allowing researchers to understand the complex responses of biological systems to the space environment. GeneLab data will potentially be useful for the development of countermeasures, monitoring the microbes that colonize the space station, understanding how plants (food) could be modified to grow better in space, and unraveling the responses of humans and other organisms to the combined effects of altered gravity and space radiation.