pairs.CSP {rflowcyt} | R Documentation |
A pairs plotting of histograms and rectangular-binned or
hexagonal-binned image plots are produced using hist
and
ContourScatterPlot
, respectively.
pairs.CSP(x, status=NULL, box.idx.list=NULL, type.CSP=c("count.diff", "p.hat", "p.hat.norm", "z.stat"), alternate.hexbinplot=FALSE, n.hexbins=100, range.x=range(x), varlabpos=round(seq(range.x[1], ceiling(diff(range.x)/150)*150+range.x[1], by=150),0), cutoffs = seq(range.x[1], ceiling(diff(range.x)/25)*25+range.x[1], by=25), labels = colnames(x), panel = ContourScatterPlot, main="", image.col=heat.colors(10), numlev=5,..., lower.panel = legend.CSP, upper.panel = panel, overlay.panel=rect.box.idx, border.boxes=1:length(box.idx.list), lwd.boxes=rep(3,length(box.idx.list)), lty.boxes=rep(1,length(box.idx.list)), label.pos = 0.5, cex.labels = NULL, font.labels = 1, row1attop = TRUE, gap=1, ch.col=c("heat.colors(n)", "rainbow(n, start=.7, end=.1)", "terrain.colors(n)", "topo.colors(n)", "cm.colors(n)"))
x |
matrix of data in which the columns are the variables and the rows are the individual observations |
status |
numerical binary 0, 1 vector denoting the status of the observations; default is NULL |
box.idx.list |
a list of vectors indicating the positions of 'x' which form a box to be overlayed on the binned plot in the upper and lower panels of the hexbin plot and the only the upper panel of the rectangular-binned plot by default |
type.CSP |
character string denoting the type of value to be estimated using the 'status' for each cell grid: the difference in counts ("count.diff"), the proportion ("p.hat"), the normalized proportion at 0.5 ("p.hat.norm"), the z.statistic ("z.stat"), see make.density for details. |
alternate.hexbinplot |
Boolean; if TRUE then alternate hexbin pairs plot is used; otherwise the ContourScatterPlot with rectangular bins is implemented |
n.hexbins |
number of bins for hexbin call; default is 100 |
range.x |
vector denoting the min and the max of the observation values across all variable columns |
varlabpos |
vector of position of the variable values in which to label the x and y axes |
cutoffs |
the cutoffs for the x and y axes of the rectangular bins when alternate.hexbinplot is FALSE |
labels |
the labels for the diagonals when alternative.hexbinplot is TRUE |
panel |
default panel function; currently this is the contour scatter plot with rectangular bins; this option is ignored when 'alternate.hexbinplot' is TRUE |
main |
the main title for the rectanglar Contour scatter plot when alternative.hexbinplot is FALSE |
image.col |
image colors for the rectangular bins when alternative.hexbinplot is FALSE |
numlev |
number of levels for the contours for the rectangular bins when alternative.hexbinplot is FALSE |
... |
other options in hexagons or ContourScatterPlot |
lower.panel |
function for the lower panels of the pairs plot; currently this is fixed as a hexbin (when 'alternate.hexbinplot' is TRUE) or the legend.CSP (when 'alternative.hexbinplot' is FALSE) |
upper.panel |
function for the upper panels of the pairs plot; currently this is fixed as a hexbin or contour scatter plot |
overlay.panel |
Function which describes the overlay image on the panels; currently this option only works with the 'rect.box.idx' function and other functions that have the same signature |
border.boxes |
vector of corresponding border colors for each of the boxes in 'box.idx.list' |
lwd.boxes |
vector of corresponding widths for each of the outlined boxes in 'box.idx.list'; default is for all the boxes to have lwd = 3 |
lty.boxes |
vector of corresponding line types for each of the outlined boxes in 'box.idx.list'; default is for all the boxes to have lty = 1 |
label.pos |
position of the labels on the diagonal panels which are currently fixed as histograms; this option is not in use currently. |
cex.labels |
cex for the labels, used only when 'alternative.hexbinplot' is TRUE |
font.labels |
font for the labels, used only when 'alternative.hexbinplot' is TRUE |
row1attop |
boolean if row 1 is at the top, used only when 'alternative.hexbinplot' is TRUE |
gap |
used only when 'alternative.hexbinplot' is TRUE |
ch.col |
character string denoting the type of color palette used for the rectangular-binned image to be displayed in the legend when 'aternate.hexbinplot' is FALSE; default is "heat.colors(n)" |
There are no legends for the hexagonal (when 'alternate.hexbinplot' is TRUE) but there is a roughly estimate legend available for the rectangular binning (when 'alternate.hexbinplot' is FALSE) in the pairs plot.
A pairs plot is displayed. NOTE: The histograms on the diagonals are of the whole dataset regardless of the value of the cells in each ContourScatterPlot.
J.Y. Wan and A.J. Rossini
Hexbin, other papers.
objects to See Also as 'hexbin' in the hexbin package
if (interactive()){ if (require(rfcdmin)){ data.there<-is.element(c("st.1829", "unst.1829", "st.DRT", "unst.DRT"),objects()) if ( ( sum(data.there) != length(data.there) )){ ## obtaining the FCS objects from VRC data data(VRCmin) } ## subsetting the data for quicker plot display of less data data.mat1<-st.DRT@data[1:10000, 1:5] ## hexagonal binning pairs.CSP(data.mat1, alternate.hexbinplot=TRUE) ## rectangular binning with legends pairs.CSP(data.mat1, numlev=3, image.col=heat.colors(20)) ## rectangular binning without legends pairs.CSP(data.mat1, numlev=3, image.col=heat.colors(20), lower.panel=ContourScatterPlot) ## putting a box around the observations ## greater than 500 for the second variable ## less than 200 for the first variable idx1<-which(data.mat1[,2] > 500) ## green box idx2<-which(data.mat1[,1] < 200) ## blue box box.idx.list<-list(idx1, idx2) ## hexbin plots pairs.CSP(data.mat1, box.idx.list=box.idx.list, alternate.hexbinplot=TRUE, border.vec=c("green", "blue")) ## rectangular binned plots pairs.CSP(data.mat1, box.idx.list=box.idx.list, alternate.hexbinplot=FALSE,border.vec=c("green", "blue"), lower.panel=ContourScatterPlot) } }