plotSampleFeatures | R Documentation |
Plot 2D-features scatter-plot of all particles. Grey color (label=0) is for data to cleaned or to remove in classification process.
plotSampleFeatures( data, label, parH = NULL, parV = NULL, figure.title = "Scatter plot", logscale = "", cex = 0.8, point.param = expand.grid(col = c("grey", "black", "red", "blue", "green", "cyan", "yellow", "orange", "rosybrown", "palevioletred", "darkblue", "deeppink", "blueviolet", "darkgoldenrod1", "chartreuse", "darkorchid1", "deeppink", "coral", "darkolivegreen1", "#66C2A5", "#9DAE8C", "#D49A73", "#F08F6D", "#C79693", "#9E9DBA", "#9F9BC9", "#C193C6", "#E28BC3", "#D2A29F", "#BABF77", "#AAD852", "#CBD844", "#ECD836", "#FAD53E", "#F1CD64", "#E7C689", "#D7BF9C", "#C5B9A7", "#B3B3B3", "#D53E4F", "#E04F4A", "#EB6046", "#F47346", "#F88B51", "#FBA35C", "#FDB869", "#FDCA79", "#FDDD88", "#F6E68F", "#EDEE93", "#E2F398", "#CDEA9D", "#B7E2A1", "#A0D8A4", "#86CEA4", "#6DC4A4", "#58B2AB", "#459DB4", "#3288BD"), pch = c(20, 0:18), stringsAsFactors = FALSE), env.plot = NULL )
data |
matrix or data.frame of raw data (points by line). |
label |
vector of labels. |
parH |
character vector specifying the name of the feature to use as x-axis. |
parV |
character vector specifying the name of the feature to use as y-axis. |
figure.title |
character vector specifying the title of the scatter-plot. |
logscale |
character vector containing "x" if the x-axis is to be logarithmic, "y" if the y-axis is to be logarithmic and "xy" or "yx" if both axes are to be logarithmic. |
cex |
numeric value specifying the size of the graphical labels. |
point.param |
data.frame specifying the colors and the symbols to use for clusters display. |
env.plot |
environment where to store graphical parameters used by function PlotScatter to select points. |
plotSampleFeatures plots 2D-features scatter-plot of all particles
None
plotProfile
, visualizeSampleClustering
dat <- rbind(matrix(rnorm(100, mean = 2, sd = 0.3), ncol = 2), matrix(rnorm(100, mean = 4, sd = 0.3), ncol = 2), matrix(rnorm(100, mean = 6, sd = 0.3), ncol = 2)) colnames(dat) <- c("x","y") tf1 <- tempfile() write.table(dat, tf1, sep=",", dec=".") sig <- data.frame(ID=rep(1:150, each=30), SIGNAL=rep(dnorm(seq(-2,2,length=30)),150)) tf2 <- tempfile() write.table(sig, tf2, sep=",", dec=".") x <- importSample(file.features=tf1, file.profiles=tf2) res <- KmeansQuick(x$features$initial$x, K=3) new.labels <- formatLabelSample(res$cluster, x) plotSampleFeatures(x$features$initial$x, label = new.labels, parH="x", parV="y")
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