cellProfiles: Cell Profiles

In ta-cameron/Cell-Profiles: Generate Cell Profile Demographs

Cell Profiles

Description

cellProfiles processes fluorescence intensity profiles from, eg, ImageJ, and prepares them for graphing as length-ordered demographs by ggplot

Usage

cellProfiles(data = NULL, position = "center", align = "native",
  reverse = FALSE, contrast = "native", range = c(0.02, 0.98))

Arguments

data	wide-formated input data consisting of paired columns depicting (1) fluorescent intensity and (2) cell length. Accepts output directly from, eg, ImageJ
position	character string (default is "left"), matching either "left" or "center". Determines alignment of stacked profiles
align	character string (default is "native"), matching either "native", "orient", or "random", OR to reuse previous alignments, the results of a prior 'cellProfiles()' run. Determines orientations of individual profiles.
reverse	logical (default is FALSE). Globally reverses alignment of profiles.
contrast	character string (default is "native"), matching either "native", "norm", or "max". Controls contrast of individual profiles; "norm" and "max" assist in visualizing profiles with heterogeneous intensity levels
range	vector of length 2 (default is c(0.02,0.98) ), defining the lower and upper percentile boundaries of the color scale. Equivalent to adjusting the min/max displayed contrast in ImageJ

Value

a list of the following values:

interpolated	processed interpolated data using supplied range values. Columns consist of: x: fluorescence profile x-coordinates intensity: fluorescence profile value y: cell number / total cells. Ordered by height for demograph plots
native	as above, but using native resolution
proportional	as above, with absolute cell length converted to fraction of cell length
wide	wide-formatted table for human eyes; NOT for ggplot2
fliplist	a simple vector that records orientations of each cell profile

See Also

The cellProfiles vignette for detailed usage instructions: vignette("cellProfiles")

cellProfileTruncate for trimming input

ggplot for plotting output

Examples

#calculate cell profiles
data_path <- system.file("extdata", "ftsZ_profiles.csv", package = "cellProfiles")
dtable <- read.table(data_path, header=FALSE, sep=",")
profileResults <- cellProfiles(data=dtable)

#calculate cell profiles, orienting brightest poles on the right & normalizing cell-cell contrast
profileResults <- cellProfiles(data=dtable, align="orient", reverse=TRUE, contrast="norm")

#plot with ggplot
ggplot2::ggplot(data=profileResults$interpolated, mapping=aes(x=x, y=y, fill=intensity, color=intensity) ) + geom_tile() + theme_classic() + scale_y_continuous(expand=c(0.0,0.0), breaks=seq(0,1,0.25), trans="reverse") + scale_fill_gradient(na.value = NA) + scale_color_gradient(na.value=NA) + labs(x="distance from midcell (um)", y="fraction of cell cycle")

ta-cameron/Cell-Profiles documentation built on July 30, 2023, 8:50 a.m.