plotOnSAM {beadarray} | R Documentation |
Function to show how quantities vary across all 96 arrays. eg mean intensity of a certain control probe
plotOnSAM(values, mx = max(values, na.rm = TRUE), scale = max(values, na.rm = TRUE), min = 0, main = NULL, label = TRUE, missing_arrays = NULL, colour=TRUE)
values |
vector containing 96 numeric values to plot |
mx |
maximum value to display on y axis of plot |
scale |
numeric value giving the amount by which to divide all numbers by (eg for log2 intensities this should be 16) to transform to range 0 - 1 |
min |
numeric value giving the minimum value to display on y axis |
main |
character string giving a title for the plot |
label |
boolean defining if the arrays are labeled on the plot |
missing_arrays |
vector of numeric values specifying the index of any arrays that have been removed from the SAM. |
colour |
if TRUE the hexagons will be plotted in colour |
Two plots are produced side-by-side. The first is a plot of the set of values against the index 1-96 and secondly we plot 8 x 12 hexagonal arrays with array number 1 being the hexagon in the top-left corner and array 96 in the bottom-right. The colour of hexagon is directly related to the value in v for the particular array number. An array which has a higher value in v will be coloured brighter.
Plot is produced on current graphical device.
Mark Dunning