florets {SpatialDecon} | R Documentation |
Draws a scatterplot where each point is a circular barplot, intended to show decon results
florets( x, y, b, col = NULL, legendwindow = FALSE, rescale.by.sqrt = TRUE, border = NA, add = FALSE, cex = 1, bty = "n", xaxt = "n", yaxt = "n", xlab = "", ylab = "", ... )
x |
Vector of x coordinates |
y |
Vector of y coordinates |
b |
matrix or cell abundances, with columns aligned with the elements of x and y |
col |
vector of colors, aligned to the rows of b. |
legendwindow |
Logical. If TRUE, the function draws a color legend in a new window |
rescale.by.sqrt |
Logical, for whether to rescale b by its square root to make value proportional to shape area, not shape length. |
border |
Color of pie segment border, defauls to NA/none |
add |
Logical. If TRUE, the function draws florets atop an existing graphics device (TRUE) or call a new device (FALSE). |
cex |
Floret size. Florets are scaled relative to the range of x and y; this further scales up or down. |
bty |
bty argument passed to plot() |
xaxt |
xaxt argument passed to plot() |
yaxt |
yaxt argument passed to plot() |
xlab |
xlab, defaults to "" |
ylab |
ylab, defaults to "" |
... |
additional arguments passed to plot() |
Draws a coxcomb plot, returns no data.
data(mini_geomx_dataset) data(safeTME) # estimate background: mini_geomx_dataset$bg <- derive_GeoMx_background( norm = mini_geomx_dataset$normalized, probepool = rep(1, nrow(mini_geomx_dataset$normalized)), negnames = "NegProbe" ) # run basic decon: res0 <- spatialdecon( norm = mini_geomx_dataset$normalized, bg = mini_geomx_dataset$bg, X = safeTME ) # draw florets: florets( x = mini_geomx_dataset$annot$x, y = mini_geomx_dataset$annot$y, b = res0$beta, cex = 2 )