Chase Clark chasemc
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| plot(protein_peak_dend$dendrogram ) | |
| z<-sapply(protein_peak_data, function(x) x@mass[x@mass > 4000 & x@mass < 15000]) | |
| z <- z[ match(labels(protein_peak_dend$dendrogram),labels(z))] | |
| plot(1, xlim=c(0,861), ylim=c(4000,15000)) | |
| for(i in seq_along(z)) points(z[[i]], x=rep(i, length(z[[i]])), col = rgb(red = 0, green = 0, blue = 0, alpha = 0.1), pch=16, cex=.5) |
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| server <- function(input, output, server) { | |
| output$out <- renderText({ | |
| validate( | |
| need(input$x < 0, "x can not be negative"), | |
| need(input$trans %in% c("log", "square-root"), "trans blah blah") | |
| ) | |
| switch(input$trans, | |
| square = input$x ^ 2, | |
| "square-root" = sqrt(input$x), |
chasemc
/ covid_by_state.R
Created
June 19, 2020 21:09
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| library(ggplot2) | |
| library(data.table) | |
| library(geofacet) | |
| library(magrittr) | |
| raw_data <- data.table::fread("http://covidtracking.com/api/states/daily.csv") | |
| raw_data$date <- as.Date(as.character(raw_data$date), "%Y%m%d") | |
| raw_data <- raw_data[date > "2020-03-15", ] |
chasemc
/ covid_by_state_loess.R
Created
June 19, 2020 20:42
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| library(ggplot2) | |
| library(data.table) | |
| library(geofacet) | |
| raw_data <- data.table::fread("http://covidtracking.com/api/states/daily.csv") | |
| raw_data$date <- as.Date(as.character(raw_data$date), "%Y%m%d") | |
| raw_data <- raw_data[date > "2020-03-15", ] | |
| raw_data[positiveIncrease > 0, ] %>% |
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| library(ggplot2) | |
| library(data.table) | |
| library(geofacet) | |
| raw_data <- data.table::fread("http://covidtracking.com/api/states/daily.csv") | |
| raw_data$date <- as.Date(as.character(raw_data$date), "%Y%m%d") | |
| raw_data <- raw_data[date > "2020-03-15", ] |
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| library(data.table) | |
| library(reshape2) | |
| library(ggplot2) | |
| a <- "https://covidtracking.com/api/v1/states/IL/daily.csv" | |
| a <- data.table::fread(a) | |
| a$date <- as.Date(as.character(a$date), "%Y%m%d") |
chasemc
/ lca_height.R
Last active
May 7, 2020 22:40
Find the height of the least common ancestor of two nodes in a dendrogram in R (requires dendextend package)
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| # install.packages("dendexted") | |
| lca_height <- function(dend, | |
| input_a, | |
| input_b) { | |
| subtrees <- dendextend::partition_leaves(dend) | |
| find_ancestors <- function(input_labels) { | |
| which(sapply(subtrees, function(x) input_labels %in% x)) |
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| protein | average | |
|---|---|---|
| RL29 [M+2H]2+ | 3637.8 | |
| RS32 [M+H]+ | 5096.8 | |
| RS34 [M+H]+ | 5381.4 | |
| RS33meth [M+H]+ | 6255.4 | |
| RL29 [M+H]+ | 7274.5 | |
| RS19 [M+H]+ | 10300.1 | |
| RNAse A [M+H]+ | 13683.2 | |
| Myoglobin [M+H]+ | 16952.3 |
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| N=5 | |
| for( i in 1:(N-1) ){ | |
| for( j in (i+1):N ){ | |
| print(paste(i,j)) | |
| } | |
| } |
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| library(ggplot2) | |
| library(data.table) | |
| library(geofacet) | |
| library(grid) | |
| library(gganimate) | |
| # Accessed 2020-03-24 at 9pm CST | |
| confirmed <- data.table::fread("http://covidtracking.com/api/states/daily.csv") | |
| confirmed$date <- as.Date(as.character(confirmed$date), "%Y%m%d") | |
| confirmed <- confirmed[confirmed$date != "2020-03-24", ] |