## ----setup, include=FALSE-----------------------------------------------------
knitr::opts_chunk$set(echo = TRUE)

## ----cache=TRUE---------------------------------------------------------------
library("dtangle")
names(shen_orr_ex)

## ----cache=TRUE---------------------------------------------------------------
head(shen_orr_ex$annotation$mixture)

## ----cache=TRUE---------------------------------------------------------------
Y <- shen_orr_ex$data$log
Y[1:4, 1:4]

## ----cache=TRUE---------------------------------------------------------------
library("dtangle")
data <- shen_orr_ex$data$log
mixture_proportions <- shen_orr_ex$annotation$mixture

## ----cache=TRUE---------------------------------------------------------------
mixture_proportions

## ----cache=TRUE---------------------------------------------------------------
pure_samples <- list(Liver = c(1, 2, 3), Brain = c(4, 5, 6), Lung = c(7, 8, 9))

dt_out <- dtangle(Y = data, pure_samples = pure_samples)

matplot(mixture_proportions, dt_out$estimates, xlim = c(0, 1), ylim = c(0, 1), xlab = "Truth", ylab = "Estimates")

## ----cache=TRUE---------------------------------------------------------------
mixture_samples <- data[-(1:9), ]
reference_samples <- data[1:9, ]

dt_out <- dtangle(Y = mixture_samples, reference = reference_samples, pure_samples = pure_samples)

mixture_mixture_proportions <- mixture_proportions[-(1:9), ]
matplot(mixture_mixture_proportions, dt_out$estimates, xlim = c(0, 1), ylim = c(0, 1), xlab = "Truth", ylab = "Estimates")

## ----cache=TRUE---------------------------------------------------------------
ref_reduced <- t(sapply(pure_samples, function(x) colMeans(reference_samples[x, , drop = FALSE])))

dt_out <- dtangle(Y = mixture_samples, reference = ref_reduced)

matplot(mixture_mixture_proportions, dt_out$estimates, xlim = c(0, 1), ylim = c(0, 1), xlab = "Truth", ylab = "Estimates")

## ----cache=TRUE---------------------------------------------------------------
dt_out <- dtangle(Y = mixture_samples, references = ref_reduced)

## ----cache=TRUE---------------------------------------------------------------
dt_out <- dtangle(Y = mixture_samples, references = ref_reduced, marker_method = "diff")

## ----cache=TRUE---------------------------------------------------------------
dt_out$n_markers

## ----cache=TRUE---------------------------------------------------------------
dt_out <- dtangle(Y = mixture_samples, references = ref_reduced, marker_method = "diff", n_markers = 100)

dt_out$n_markers

## ----cache=TRUE---------------------------------------------------------------
dt_out <- dtangle(Y = mixture_samples, references = ref_reduced, marker_method = "diff", n_markers = c(100, 150, 50))

dt_out$n_markers

## ----cache=TRUE---------------------------------------------------------------
dt_out <- dtangle(Y = mixture_samples, references = ref_reduced, marker_method = "diff", n_markers = .075)

dt_out$n_markers

dt_out <- dtangle(Y = mixture_samples, references = ref_reduced, marker_method = "diff", n_markers = c(.1, .15, .05))

dt_out$n_markers

## ----cache=TRUE---------------------------------------------------------------
marker_genes <- list(
  c(120, 253, 316),
  c(180, 429, 14),
  c(1, 109, 206)
)

dt_out <- dtangle(Y = mixture_samples, references = ref_reduced, markers = marker_genes)
dt_out$n_markers

## ----cache=TRUE---------------------------------------------------------------
mrkrs <- find_markers(Y = mixture_samples, references = ref_reduced)
names(mrkrs)

## ----cache=TRUE---------------------------------------------------------------
dt_out <- dtangle(Y = mixture_samples, references = ref_reduced, markers = mrkrs, n_markers = .1)

## ----cache=TRUE---------------------------------------------------------------
dt_out <- dtangle(Y = mixture_samples, references = ref_reduced, gamma = .9)

## ----cache=TRUE---------------------------------------------------------------
dt_out <- dtangle(Y = mixture_samples, references = ref_reduced, data_type = "microarray-gene")

## ----cache=TRUE---------------------------------------------------------------
dtangle:::gma

## ----cache=TRUE---------------------------------------------------------------
dt_out <- dtangle(Y = mixture_samples, references = ref_reduced, summary_fn = median)
head(dt_out$estimates)
dt_out <- dtangle(Y = mixture_samples, references = ref_reduced, summary_fn = mean)
head(dt_out$estimates)