Commit ea935f44 authored by dmattek's avatar dmattek

Major rev: added clustering

parent b64429ce
## Custom plotting
require(ggplot2)
rhg_cols <- c(
"#771C19",
"#AA3929",
......@@ -24,6 +26,33 @@ md_cols <- c(
"#238443"
)
s.cl.linkage = c("ward.D",
"ward.D2",
"single",
"complete",
"average",
"mcquitty",
"centroid")
s.cl.spar.linkage = c("average",
"complete",
"single",
"centroid")
s.cl.diss = c("euclidean", "maximum", "manhattan", "canberra", "binary", "minkowski")
s.cl.spar.diss = c("squared.distance","absolute.value")
l.col.pal = list(
"White-Orange-Red" = 'OrRd',
"Yellow-Orange-Red" = 'YlOrRd',
"Reds" = "Reds",
"Oranges" = "Oranges",
"Greens" = "Greens",
"Blues" = "Blues",
"Spectral" = 'Spectral'
)
myGgplotTraj = function(dt.arg,
x.arg,
y.arg,
......@@ -115,16 +144,16 @@ myGgplotTraj = function(dt.arg,
userDataGen <- function() {
cat(file=stderr(), 'userDataGen: in\n')
locNtp = 13
locNtp = 40
locNtracks = 5
locNsites = 4
locNwells = 2
dt.nuc = data.table(Metadata_Site = rep(1:locNsites, each = locNtp * locNtracks),
Metadata_Well = rep(1:locNwells, each = locNtp * locNsites * locNtracks / locNwells),
Metadata_Time = rep(1:locNtp, locNsites* locNtracks),
meas_MeanIntensity_cyto = rnorm(locNtp * locNtracks * locNsites, .5, 0.1),
meas_MeanIntensity_nuc = rnorm(locNtp * locNtracks * locNsites, .5, 0.1),
Metadata_RealTime = rep(1:locNtp, locNsites* locNtracks),
objCyto_Intensity_MeanIntensity_imErkCor = rnorm(locNtp * locNtracks * locNsites, .5, 0.1),
objNuc_Intensity_MeanIntensity_imErkCor = rnorm(locNtp * locNtracks * locNsites, .5, 0.1),
TrackLabel = rep(1:(locNtracks*locNsites), each = locNtp))
cat(colnames(dt.nuc))
......@@ -190,3 +219,21 @@ myNorm = function(in.dt,
loc.dt[, c('meas.md', 'meas.mad') := NULL]
return(loc.dt)
}
myGgplotTheme = theme_bw(base_size = 18, base_family = "Helvetica") +
theme(
panel.grid.minor = element_blank(),
panel.grid.major = element_blank(),
axis.line.x = element_line(color = "black", size = 0.25),
axis.line.y = element_line(color = "black", size = 0.25),
axis.text.x = element_text(size = 12, angle = 45, hjust = 1),
axis.text.y = element_text(size = 12),
strip.text.x = element_text(size = 14, face = "bold"),
strip.text.y = element_text(size = 14, face = "bold"),
strip.background = element_blank(),
legend.key = element_blank(),
legend.key.height = unit(1, "lines"),
legend.key.width = unit(2, "lines"),
legend.position = "right"
)
\ No newline at end of file
source('auxfunc.R')
\ No newline at end of file
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