In nbenn/singleCellFeatures: Analyze single cell features stored in an openBIS instance

suppressPackageStartupMessages(library(knitr))
suppressPackageStartupMessages(library(singleCellFeatures))
options(scipen=1, digits=2, singleCellFeatures.progressBars="none")
opts_chunk$set(fig.height=8, fig.width=12)

Several coordination augmentation features have been implemented. While the previous two vignettes showed off some of them, this one summarizes all available newly generated coordinate features.

features <- c("^Image.Count_Cells$",
              "^Nuclei.AreaShape_Area$",
              "^Nuclei.AreaShape_FormFactor$",
              "^Cells.Location_Center_X$",
              "^Cells.Location_Center_Y$",
              "^Cells.AreaShape_Area$",
              "^Cells.Intensity_MeanIntensity_CorrPathogen$",
              "^Cells.Intensity_StdIntensity_CorrPathogen$",
              "^Nuclei.Intensity_MeanIntensity_CorrPathogen$",
              "^Nuclei.Intensity_StdIntensity_CorrPathogen$")
data.red <- PlateData(PlateLocation("J107-2C"), select=features)
data.aug <- augmentImageLocation(data.red)
data.aug <- augmentCordinateFeatures(data.aug, 5, c(14, 10), TRUE, TRUE)
molten   <- meltData(data.aug)
cells    <- molten$mat$Cells
thin <- sample.int(nrow(cells), nrow(cells) / 20)
vlines <- data.frame(c(0, 1397, 2799, 4196))
hlines <- data.frame(c(0, 1045, 2095, 3140))
names(vlines) <- "border"
names(hlines) <- "border"

ggplot(cells[thin,], aes(x=Cells.Location_Shifted_X,
                         y=Cells.Location_Shifted_Y)) +
  geom_point(aes(colour=Cells.Location_Dist_Center_Image)) +
  scale_colour_gradientn(colours=brewer.pal(9, "YlGnBu"),
    guide=guide_colourbar(title="Distance from image center", 
                          barwidth=25, barheight=2)) +
  theme_bw(base_size=18) +
  theme(legend.position="bottom", axis.title=element_blank(),
        axis.text=element_blank(), axis.ticks=element_blank(),
        line=element_blank()) +
  ggtitle("Cell location and distance from image center") +
  geom_vline(data=vlines, aes(xintercept=border)) +
  geom_hline(data=hlines, aes(yintercept=border))

ggplot(cells[thin,], aes(x=Cells.Location_Shifted_X,
                         y=Cells.Location_Shifted_Y)) +
  geom_point(aes(colour=Cells.Location_Dist_Center_Well)) +
  scale_colour_gradientn(colours=brewer.pal(9, "YlGnBu"),
    guide=guide_colourbar(title="Distance from well center",
                          barwidth=25, barheight=2)) +
  theme_bw(base_size = 18) +
  theme(legend.position="bottom", axis.title=element_blank(),
        axis.text=element_blank(), axis.ticks=element_blank(),
        line=element_blank()) +
  ggtitle("Cell location and distance from well center") +
  geom_vline(data=vlines, aes(xintercept=border)) +
  geom_hline(data=hlines, aes(yintercept=border))

ggplot(cells[thin,], aes(x=Cells.Location_Shifted_X,
                         y=Cells.Location_Shifted_Y)) +
  geom_point(aes(colour=factor(Cells.Location_Facet_Type))) +
  scale_colour_brewer(palette="YlGnBu",
                      guide=guide_legend(title="Facet type", nrow=2),
                      labels=c("no border", "inward border", "inward edge",
                               "outward border", "both borders",
                               "outward edge")) +
  theme_bw(base_size = 18) +
  theme(legend.position="bottom", axis.title=element_blank(),
        axis.text=element_blank(), axis.ticks=element_blank(),
        line=element_blank()) +
  ggtitle("Cell location and facet type") +
  geom_vline(data=vlines, aes(xintercept=border)) +
  geom_hline(data=hlines, aes(yintercept=border))

ggplot(cells[thin,], aes(x=Cells.Location_Shifted_X,
                         y=Cells.Location_Shifted_Y)) +
  geom_point(aes(colour=Cells.Location_Facet_X_Well)) +
  scale_colour_gradientn(colours=brewer.pal(9, "YlGnBu"),
    guide=guide_colourbar(title="Facet number", barwidth=25, barheight=2)) +
  theme_bw(base_size = 18) +
  theme(legend.position="bottom", axis.title=element_blank(),
        axis.text=element_blank(), axis.ticks=element_blank(),
        line=element_blank()) +
  ggtitle("X-coord facet number (well)") +
  geom_vline(data=vlines, aes(xintercept=border)) +
  geom_hline(data=hlines, aes(yintercept=border))

ggplot(cells[thin,], aes(x=Cells.Location_Shifted_X,
                         y=Cells.Location_Shifted_Y)) +
  geom_point(aes(colour=Cells.Location_Facet_Y_Well)) +
  scale_colour_gradientn(colours=brewer.pal(9, "YlGnBu"),
    guide=guide_colourbar(title="Facet number", barwidth=25, barheight=2)) +
  theme_bw(base_size = 18) +
  theme(legend.position="bottom", axis.title=element_blank(),
        axis.text=element_blank(), axis.ticks=element_blank(),
        line=element_blank()) +
  ggtitle("Y-coord facet number (well)") +
  geom_vline(data=vlines, aes(xintercept=border)) +
  geom_hline(data=hlines, aes(yintercept=border))

ggplot(cells[thin,], aes(x=Cells.Location_Shifted_X,
                         y=Cells.Location_Shifted_Y)) +
  geom_point(aes(colour=factor(Cells.Location_In_Ellipse_Image))) +
  scale_colour_brewer(name="Ellipses", palette="YlGnBu") +
  theme_bw(base_size = 18) +
  theme(legend.position="bottom", axis.title=element_blank(),
        axis.text=element_blank(), axis.ticks=element_blank(),
        line=element_blank()) +
  ggtitle("Cell location and image ellipse membership") +
  geom_vline(data=vlines, aes(xintercept=border)) +
  geom_hline(data=hlines, aes(yintercept=border))

ggplot(cells[thin,], aes(x=Cells.Location_Shifted_X,
                         y=Cells.Location_Shifted_Y)) +
  geom_point(aes(colour=factor(Cells.Location_In_Ellipse_Well))) +
  scale_colour_brewer(name="Ellipses", palette="YlGnBu") +
  theme_bw(base_size = 18) +
  theme(legend.position="bottom", axis.title=element_blank(),
        axis.text=element_blank(), axis.ticks=element_blank(),
        line=element_blank()) +
  ggtitle("Cell location and well ellipse membership") +
  geom_vline(data=vlines, aes(xintercept=border)) +
  geom_hline(data=hlines, aes(yintercept=border))

ggplot(cells[cells$Well.Name == "H6",], aes(x=Cells.Location_Shifted_X,
                                            y=Cells.Location_Shifted_Y)) +
  geom_point(aes(colour=factor(Cells.Location_Facet_Border)), size=4) +
  scale_colour_brewer(name="Non-empty neighbor facets", palette="YlGnBu") +
  theme_bw(base_size = 18) +
  theme(legend.position="bottom", axis.title=element_blank(),
        axis.text=element_blank(), axis.ticks=element_blank(),
        line=element_blank()) +
  ggtitle("Cell location and facet borders") +
  geom_vline(data=vlines, aes(xintercept=border)) +
  geom_hline(data=hlines, aes(yintercept=border))

ggplot(cells[cells$Well.Name == "H6",], aes(x=Cells.Location_Shifted_X,
                                            y=Cells.Location_Shifted_Y)) +
  geom_point(aes(colour=Cells.Location_Kern_Dens_Image), size=4) +
  scale_colour_gradientn(colours=brewer.pal(9, "YlGnBu"),
    guide=guide_colourbar(title="Cell density", barwidth=25, barheight=2)) +
  theme_bw(base_size = 18) +
  theme(legend.position="bottom", axis.title=element_blank(),
        axis.text=element_blank(), axis.ticks=element_blank(),
        line=element_blank()) +
  ggtitle("Cell location and cell density") +
  geom_vline(data=vlines, aes(xintercept=border)) +
  geom_hline(data=hlines, aes(yintercept=border))

nbenn/singleCellFeatures documentation built on May 23, 2019, 12:24 p.m.