Plot surface texture parameters for data mining
Ivan Calandra
2020-01-21 09:06:18
Rbin-file used for this script: ~/Data/brushing_v2.Rbin
1. Goal of the script
The script will plot all variables to see which ones should be used for further analysis.
Scatterplot of each variable will be plotted.
All plots will be saved in a subfolder “Plots” within the directory of the present Rmd file, i.e. “~/Plots”.
3. Load data into R object
The imported file is: “~/Data/brushing_v2.Rbin”
Its modification, ‘last status change’ (= ‘creation’ on Windows) and last access times are, respectively: “2020-01-21 08:58:08”, “2020-01-21 08:58:08” and “2020-01-21 08:58:08”.
4. Prepare variables
4.1. Define numeric variables
The following variables will be used:
[21] epLsar
[22] Asfc
[23] Smfc
[24] HAsfc9
[25] HAsfc81
[26] Sq.SL
[27] Ssk.SL
[28] Sku.SL
[29] Sp.SL
[30] Sv.SL
[31] Sz.SL
[32] Sa.SL
[33] Smr.SL
[34] Smc.SL
[35] Sxp.SL
[36] Sal.SL
[37] Str.SL
[38] Std.SL
[39] Sdq.SL
[40] Sdr.SL
[41] Vm.SL
[42] Vv.SL
[43] Vmp.SL
[44] Vmc.SL
[45] Vvc.SL
[46] Vvv.SL
[47] Maximum.depth.of.furrows.SL
[48] Mean.depth.of.furrows.SL
[49] Mean.density.of.furrows.SL
[50] Isotropy.SL
[51] First.Direction.SL
[52] Second.Direction.SL
[53] Third.Direction.SL
[54] Isotropy.SL.1
[55] Periodicity.SL
[56] Period.SL
[57] Direction.of.period.SL
[58] Sq.SF
[59] Ssk.SF
[60] Sku.SF
[61] Sp.SF
[62] Sv.SF
[63] Sz.SF
[64] Sa.SF
[65] Smr.SF
[66] Smc.SF
[67] Sxp.SF
[68] Sal.SF
[69] Str.SF
[70] Std.SF
[71] Sdq.SF
[72] Sdr.SF
[73] Vm.SF
[74] Vv.SF
[75] Vmp.SF
[76] Vmc.SF
[77] Vvc.SF
[78] Vvv.SF
[79] Maximum.depth.of.furrows.SF
[80] Mean.depth.of.furrows.SF
[81] Mean.density.of.furrows.SF
[82] Isotropy.SF
[83] First.Direction.SF
[84] Second.Direction.SF
[85] Third.Direction.SF
[86] Isotropy.SF.1
[87] Periodicity.SF
[88] Period.SF
[89] Direction.of.period.SF4.2. Define grouping variable
5. Plot each of the selected numeric variable (1 plot for flint, 1 plot for quartzite)
for (i in num.var){
#plot
p <- ggplot(data=imp.data, aes_string(x="Before.after", y=names(imp.data)[i], color="Dirt", shape="Brush")) + geom_point(size=3) + geom_line(aes(group=Sample.Area))
p <- p + geom_text(aes(label=ifelse(imp.data[["Before.after"]]=="Before",gsub("FLT|QTZ","",imp.data$Sample.Area),"")), nudge_x=-0.4)
p <- p + expand_limits(x=0) + theme_classic() + facet_wrap(~Material)
print(p)
#save to PDF
file.out <- paste0(basename(file_path_sans_ext(row.names(imp.info))), "_plot_", names(imp.data)[i], ".pdf")
ggsave(filename=file.out, plot=p, path=dir.plots, device="pdf", width=21, units="cm")
}
Warning: Removed 29 rows containing missing values (geom_point).Warning: Removed 29 rows containing missing values (geom_path).Warning: Removed 29 rows containing missing values (geom_text).Warning: Removed 29 rows containing missing values (geom_point).Warning: Removed 29 rows containing missing values (geom_path).Warning: Removed 29 rows containing missing values (geom_text).
Warning: Removed 29 rows containing missing values (geom_point).Warning: Removed 29 rows containing missing values (geom_path).Warning: Removed 29 rows containing missing values (geom_text).Warning: Removed 29 rows containing missing values (geom_point).Warning: Removed 29 rows containing missing values (geom_path).Warning: Removed 29 rows containing missing values (geom_text).
Warning: Removed 29 rows containing missing values (geom_point).Warning: Removed 29 rows containing missing values (geom_path).Warning: Removed 29 rows containing missing values (geom_text).Warning: Removed 29 rows containing missing values (geom_point).Warning: Removed 29 rows containing missing values (geom_path).Warning: Removed 29 rows containing missing values (geom_text).
Warning: Removed 4 rows containing missing values (geom_point).Warning: Removed 4 rows containing missing values (geom_path).Warning: Removed 4 rows containing missing values (geom_text).Warning: Removed 4 rows containing missing values (geom_point).Warning: Removed 4 rows containing missing values (geom_path).Warning: Removed 4 rows containing missing values (geom_text).
Warning: Removed 4 rows containing missing values (geom_point).Warning: Removed 4 rows containing missing values (geom_path).Warning: Removed 4 rows containing missing values (geom_text).Warning: Removed 4 rows containing missing values (geom_point).Warning: Removed 4 rows containing missing values (geom_path).Warning: Removed 4 rows containing missing values (geom_text).
Warning: Removed 4 rows containing missing values (geom_point).Warning: Removed 4 rows containing missing values (geom_path).Warning: Removed 4 rows containing missing values (geom_text).Warning: Removed 4 rows containing missing values (geom_point).Warning: Removed 4 rows containing missing values (geom_path).Warning: Removed 4 rows containing missing values (geom_text).
The following plot(s) was (were) created and saved in “~/Plots”:
[1] "brushing_v2_plot_Asfc.pdf"
[2] "brushing_v2_plot_Direction.of.period.SF.pdf"
[3] "brushing_v2_plot_Direction.of.period.SL.pdf"
[4] "brushing_v2_plot_epLsar.pdf"
[5] "brushing_v2_plot_First.Direction.SF.pdf"
[6] "brushing_v2_plot_First.Direction.SL.pdf"
[7] "brushing_v2_plot_HAsfc81.pdf"
[8] "brushing_v2_plot_HAsfc9.pdf"
[9] "brushing_v2_plot_Isotropy.SF.1.pdf"
[10] "brushing_v2_plot_Isotropy.SF.pdf"
[11] "brushing_v2_plot_Isotropy.SL.1.pdf"
[12] "brushing_v2_plot_Isotropy.SL.pdf"
[13] "brushing_v2_plot_Maximum.depth.of.furrows.SF.pdf"
[14] "brushing_v2_plot_Maximum.depth.of.furrows.SL.pdf"
[15] "brushing_v2_plot_Mean.density.of.furrows.SF.pdf"
[16] "brushing_v2_plot_Mean.density.of.furrows.SL.pdf"
[17] "brushing_v2_plot_Mean.depth.of.furrows.SF.pdf"
[18] "brushing_v2_plot_Mean.depth.of.furrows.SL.pdf"
[19] "brushing_v2_plot_Period.SF.pdf"
[20] "brushing_v2_plot_Period.SL.pdf"
[21] "brushing_v2_plot_Periodicity.SF.pdf"
[22] "brushing_v2_plot_Periodicity.SL.pdf"
[23] "brushing_v2_plot_Sa.SF.pdf"
[24] "brushing_v2_plot_Sa.SL.pdf"
[25] "brushing_v2_plot_Sal.SF.pdf"
[26] "brushing_v2_plot_Sal.SL.pdf"
[27] "brushing_v2_plot_Sdq.SF.pdf"
[28] "brushing_v2_plot_Sdq.SL.pdf"
[29] "brushing_v2_plot_Sdr.SF.pdf"
[30] "brushing_v2_plot_Sdr.SL.pdf"
[31] "brushing_v2_plot_Second.Direction.SF.pdf"
[32] "brushing_v2_plot_Second.Direction.SL.pdf"
[33] "brushing_v2_plot_Sku.SF.pdf"
[34] "brushing_v2_plot_Sku.SL.pdf"
[35] "brushing_v2_plot_Smc.SF.pdf"
[36] "brushing_v2_plot_Smc.SL.pdf"
[37] "brushing_v2_plot_Smfc.pdf"
[38] "brushing_v2_plot_Smr.SF.pdf"
[39] "brushing_v2_plot_Smr.SL.pdf"
[40] "brushing_v2_plot_Sp.SF.pdf"
[41] "brushing_v2_plot_Sp.SL.pdf"
[42] "brushing_v2_plot_Sq.SF.pdf"
[43] "brushing_v2_plot_Sq.SL.pdf"
[44] "brushing_v2_plot_Ssk.SF.pdf"
[45] "brushing_v2_plot_Ssk.SL.pdf"
[46] "brushing_v2_plot_Std.SF.pdf"
[47] "brushing_v2_plot_Std.SL.pdf"
[48] "brushing_v2_plot_Str.SF.pdf"
[49] "brushing_v2_plot_Str.SL.pdf"
[50] "brushing_v2_plot_Sv.SF.pdf"
[51] "brushing_v2_plot_Sv.SL.pdf"
[52] "brushing_v2_plot_Sxp.SF.pdf"
[53] "brushing_v2_plot_Sxp.SL.pdf"
[54] "brushing_v2_plot_Sz.SF.pdf"
[55] "brushing_v2_plot_Sz.SL.pdf"
[56] "brushing_v2_plot_Third.Direction.SF.pdf"
[57] "brushing_v2_plot_Third.Direction.SL.pdf"
[58] "brushing_v2_plot_Vm.SF.pdf"
[59] "brushing_v2_plot_Vm.SL.pdf"
[60] "brushing_v2_plot_Vmc.SF.pdf"
[61] "brushing_v2_plot_Vmc.SL.pdf"
[62] "brushing_v2_plot_Vmp.SF.pdf"
[63] "brushing_v2_plot_Vmp.SL.pdf"
[64] "brushing_v2_plot_Vv.SF.pdf"
[65] "brushing_v2_plot_Vv.SL.pdf"
[66] "brushing_v2_plot_Vvc.SF.pdf"
[67] "brushing_v2_plot_Vvc.SL.pdf"
[68] "brushing_v2_plot_Vvv.SF.pdf"
[69] "brushing_v2_plot_Vvv.SL.pdf" R version 3.6.2 (2019-12-12)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18362)
Matrix products: default
locale:
[1] LC_COLLATE=English_United Kingdom.1252
[2] LC_CTYPE=English_United Kingdom.1252
[3] LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.1252
attached base packages:
[1] tools stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] ggplot2_3.2.1 R.utils_2.9.2 R.oo_1.23.0 R.methodsS3_1.7.1
loaded via a namespace (and not attached):
[1] Rcpp_1.0.3 knitr_1.26 magrittr_1.5 tidyselect_0.2.5
[5] munsell_0.5.0 colorspace_1.4-1 R6_2.4.1 rlang_0.4.2
[9] dplyr_0.8.3 stringr_1.4.0 grid_3.6.2 gtable_0.3.0
[13] xfun_0.11 withr_2.1.2 htmltools_0.4.0 assertthat_0.2.1
[17] yaml_2.2.0 lazyeval_0.2.2 digest_0.6.23 tibble_2.1.3
[21] lifecycle_0.1.0 crayon_1.3.4 farver_2.0.1 purrr_0.3.3
[25] glue_1.3.1 evaluate_0.14 rmarkdown_2.0 labeling_0.3
[29] stringi_1.4.3 compiler_3.6.2 pillar_1.4.2 scales_1.1.0
[33] pkgconfig_2.0.3 RStudio Version 1.2.5019
END OF SCRIPT