Plot Graph Types

Source: vignettes/AFM-graphTypes.Rmd

Loading AFM image 

fname = AFM.getSampleImages()[1]
afmd = AFM.import(fname)

The AFM image can be displayed using graphTypes:

graphType 1

This is the basic and default graph for an AFM image:

q = plot(afmd, graphType=1, trimPeaks=0.01)
#> Graphing: HeightRetrace

graphType 2

This graph has a square shape and adds a bar of length 20%; it places the scale inside the graph.

plot(afmd, graphType=2,trimPeaks=0.01)
#> Graphing: HeightRetrace

The image can be saved with ggsave as it is graphed with ggplot.

g1 = plot(afmd, graphType=2, size=10, trimPeaks=0.01)
#> Graphing: HeightRetrace
ggsave(tempfile(pattern = "", fileext = ".png"), plot=g1, dpi=150)

graphType 3

This graph type is bare and has neither length scales nor legend.

plot(afmd, graphType=3, trimPeaks=0.01)
#> Graphing: HeightRetrace

summary(afmd)
#>      objectect               description resolution           size
#> 1 Cypher image KC200, FePc, KC20170720Si  128 x 128 4000 x 4000 nm
#> 2 Cypher image KC200, FePc, KC20170720Si  128 x 128 4000 x 4000 nm
#> 3 Cypher image KC200, FePc, KC20170720Si  128 x 128 4000 x 4000 nm
#> 4 Cypher image KC200, FePc, KC20170720Si  128 x 128 4000 x 4000 nm
#>            channel history     z.min    z.max z.units dataType
#> 1    HeightRetrace         -32.45992 50.78832      nm    image
#> 2 AmplitudeRetrace          29.00730 32.78488      nm    image
#> 3     PhaseRetrace          63.92822 85.18923     deg    image
#> 4   ZSensorRetrace         -29.44336 48.16414      nm    image

graphType 4

This graph type is plain with a scale. You can also change the color and the size of the font that displays the scale.

plot(afmd, graphType=4, col='white', size=10, trimPeaks=0.05, fillOption = 'A')
#> Graphing: HeightRetrace

Red Blue Color Scheme

This graph type is bare and has neither length scales nor legend.

plot(afmd, graphType=1, trimPeaks=0.01, redBlue = TRUE)
#> Graphing: HeightRetrace

Graphing 2 plots side by side

Use the package cowplot to create a graph with two plots. Use save_plot to save the graph.

library(cowplot)
library(latex2exp)
fname2 = AFM.getSampleImages(type='ibw')[1]
afmd = AFM.import(fname2)

g1 = plot(afmd, trimPeaks=0.01, graphType = 1) + 
  labs(fill='h (nm)') + theme(legend.key.size = unit(1, 'char'))
#> Graphing: HeightRetrace
g2 = plot(afmd, no=2, trimPeaks=0.01, graphType = 1, mpt=29.6) +
  labs(fill="A (nm)") + theme(legend.key.size = unit(1, 'char'))
#> Graphing: AmplitudeRetrace
g3 = plot(afmd, no=3, trimPeaks=0.01, graphType = 1, mpt=65.5) +
  labs(fill=TeX("$\\phi$ (deg)")) + theme(legend.key.size = unit(1, 'char'))
#> Graphing: PhaseRetrace
g4 = plot(afmd, no=4, trimPeaks=0.01, graphType = 1) + 
  labs(fill="z (nm)") + theme(legend.key.size = unit(1, 'char'))
#> Graphing: ZSensorRetrace
gAll = plot_grid(g1, g2, g3, g4,
          labels=c('a','b','c','d')) 
ggdraw(add_sub(gAll, 
               "Showing surface morphology of a phthalocyanine thin film\n with (a) height h, (b) amplitude A, (c) phase ϕ, and \n (d) z-sensor z response. Sample / image from Gredig\n Lab, CSU Long Beach.",
               x=0.1, hjust=0))

Changing the Color Palette

You can use the fillOption option to change the color palette, see also ? scale_fill_viridis. There are 8 options:

plot(afmd, graphType = 1, fillOption = "magma")
#> Graphing: HeightRetrace

plot(afmd, graphType = 1, fillOption = "inferno")
#> Graphing: HeightRetrace

plot(afmd, graphType = 1, fillOption = "plasma")
#> Graphing: HeightRetrace

plot(afmd, graphType = 1, fillOption = "viridis")
#> Graphing: HeightRetrace

plot(afmd, graphType = 1, fillOption = "cividis")
#> Graphing: HeightRetrace

plot(afmd, graphType = 1, fillOption = "rocket")
#> Graphing: HeightRetrace

plot(afmd, graphType = 1, fillOption = "mako")
#> Graphing: HeightRetrace

plot(afmd, graphType = 1, fillOption = "turbo")
#> Graphing: HeightRetrace

Adjusting the scale 

plot(afmd)
#> Graphing: HeightRetrace

plot(afmd, setRange=c(-50,50))
#> Graphing: HeightRetrace