doc/diagram.R
In solarchemist/bandgaps: Band Gaps and Edges for Some Semiconductors
## ----'R-setup', echo=F, results='hide', cache=FALSE-------------------------------
options(
tikzDefaultEngine = "pdftex",
"tikzLatexPackages" = c(
"\\usepackage{tikz}\n",
"\\usepackage[active,tightpage,psfixbb]{preview}\n",
"\\PreviewEnvironment{pgfpicture}\n",
"\\setlength\\PreviewBorder{0pt}\n",
"\\usepackage{chemformula}\n",
"\\setchemformula{charge-style=math}\n",
"\\usepackage{siunitx}\n",
"\\sisetup{separate-uncertainty,detect-family,range-phrase=\\ensuremath{\\text{ to }}}\n",
"\\DeclareSIUnit{\\counts}{cts}\n",
"\\DeclareSIUnit{\\cps}{cps}\n",
"\\DeclareSIUnit{\\molar}{\\mole\\per\\cubic\\deci\\metre}\n",
"\\DeclareSIUnit{\\Molar}{\\textsc{m}}\n",
"\\DeclareSIUnit{\\vsAgCl}{vs~\\ch{Ag}/\\ch{AgCl}}",
"\\DeclareSIUnit{\\vsNHE}{vs~NHE}",
"\\DeclareSIUnit{\\vsSHE}{vs~SHE}",
"\\DeclareSIUnit{\\vsSCE}{vs~SCE}",
"\\DeclareSIUnit{\\voltAgCl}{\\volt\\vsAgCl}",
"\\DeclareSIUnit{\\voltNHE}{\\volt\\vsNHE}",
"\\DeclareSIUnit{\\voltSHE}{\\volt\\vsSHE}",
"\\DeclareSIUnit{\\voltSCE}{\\volt\\vsSCE}"),
digits = 7,
width = 84,
continue = " ",
prompt = "> ",
stringsAsFactors = FALSE)
# here::i_am("vignettes/diagram.Rnw")
## ----'load-R-packages', echo=F, results='hide', message=FALSE---------------------
library(bandgaps)
# packages listed below should also be listed in DESCRIPTION
library(common)
# library(here)
# library(git2r)
# repo <- repository(here())
library(graphics)
library(ggplot2)
# library(ggrepel) # am I using it?
library(dplyr)
library(tidyr)
library(xtable)
library(knitr)
opts_knit$set(
self.contained = FALSE,
child.path = '')
opts_chunk$set(
dev = 'tikz',
# external = TRUE only takes effect when tikz is the ONLY dev option
external = TRUE,
cache = FALSE,
fig.width = 3.40, # 2.60,
# corresponding height based on golden ratio (1.618034):
# W 3.54 ==> H 2.19 >> works better >> W 2.60, H 1.61
# W 5.51 ==> H 3.41
# W 7.48 ==> H 4.62 >> works better >> W 5.40, H 3.34
fig.height = 2.10, # 1.61,
out.width = '3.40in', # '2.60in',
fig.align = 'center',
# size affects all knitr output. We use it primarily
# to match knitr font size to figure captions
size = 'footnotesize',
echo = FALSE,
eval = TRUE,
results = 'hide',
message = FALSE,
tidy = FALSE)
## ----ref.label='bandgaps-plot-figure', echo=TRUE, eval=FALSE----------------------
# plot_bandgaps(bandgaps::semiconductors %>% filter(Nernstian == TRUE))
## ----'bandgaps-plot-figure', fig.width=6, fig.height=3.71, out.width='6in'--------
plot_bandgaps(bandgaps::semiconductors %>% filter(Nernstian == TRUE))
## ----'bandgaps-ggplot-figure', fig.width=6, fig.height=3.71, out.width='6in'------
ggplot_materials <-
bandgaps::semiconductors %>%
# for recalculation of pH, only display Nernstian semiconductors
filter(class == "oxide")
ggplot_materials <-
ggplot_materials %>%
# add column with x variable
# NOTE: do this as the last step to avoid weird visual gaps
# 0.4 is the x-value of the first line, stepsize 1.0
mutate(x = seq(0.4, dim(ggplot_materials)[1], by = 1.0))
ggplot(data = ggplot_materials) +
# water redox lines
geom_hline(yintercept = 0.00, colour = "red", linetype = "dashed", size = 0.3) +
geom_hline(yintercept = 1.23, colour = "blue", linetype = "dashed", size = 0.3) +
# band gaps visualised as vertical lines
geom_linerange(
aes(x = x, ymin = CB, ymax = VB),
size = 0.8) +
# label each compound
geom_text(
aes(
x = x,
label = paste0("\\ch{", formula, "}"),
# can we put the label at VB if CB > than some value?
# also add a constant space between CB/VB and label
y = ifelse(CB > -0.5, CB - 0.05, VB + 0.05),
# left-adjust labels at CB, and right-adjust labels at VB
hjust = ifelse(CB > -0.5, 0, 1)),
size = 3,
vjust = 0.5,
angle = 80) +
# flip primary y-axis and create secondary AVS axis
scale_y_continuous(
name = "E(SHE)/V",
# make sure each unit step is marked
breaks = seq(-4, 6),
# expand() parameters are
# a multiplicative and an absolute expansion
# we add some space to make sure the labels of the largest Eg fits
expand = c(0, 0.65),
trans = "reverse",
sec.axis =
# note the initial minus sign
# which makes the AVS scale go positive up
sec_axis(
~ -. + refelectrodes::as.SHE(0, scale = "AVS"),
name = "E(AVS)/V")) +
# a more suitable theme
theme_classic() +
# completely remove the x-axis
theme(
axis.text.x = element_blank(),
axis.title.x = element_blank(),
axis.line.x = element_blank(),
axis.ticks.x = element_blank())
## ----ref.label='bandgaps-ggplot-figure', echo=TRUE, eval=FALSE--------------------
# ggplot_materials <-
# bandgaps::semiconductors %>%
# # for recalculation of pH, only display Nernstian semiconductors
# filter(class == "oxide")
# ggplot_materials <-
# ggplot_materials %>%
# # add column with x variable
# # NOTE: do this as the last step to avoid weird visual gaps
# # 0.4 is the x-value of the first line, stepsize 1.0
# mutate(x = seq(0.4, dim(ggplot_materials)[1], by = 1.0))
# ggplot(data = ggplot_materials) +
# # water redox lines
# geom_hline(yintercept = 0.00, colour = "red", linetype = "dashed", size = 0.3) +
# geom_hline(yintercept = 1.23, colour = "blue", linetype = "dashed", size = 0.3) +
# # band gaps visualised as vertical lines
# geom_linerange(
# aes(x = x, ymin = CB, ymax = VB),
# size = 0.8) +
# # label each compound
# geom_text(
# aes(
# x = x,
# label = paste0("\\ch{", formula, "}"),
# # can we put the label at VB if CB > than some value?
# # also add a constant space between CB/VB and label
# y = ifelse(CB > -0.5, CB - 0.05, VB + 0.05),
# # left-adjust labels at CB, and right-adjust labels at VB
# hjust = ifelse(CB > -0.5, 0, 1)),
# size = 3,
# vjust = 0.5,
# angle = 80) +
# # flip primary y-axis and create secondary AVS axis
# scale_y_continuous(
# name = "E(SHE)/V",
# # make sure each unit step is marked
# breaks = seq(-4, 6),
# # expand() parameters are
# # a multiplicative and an absolute expansion
# # we add some space to make sure the labels of the largest Eg fits
# expand = c(0, 0.65),
# trans = "reverse",
# sec.axis =
# # note the initial minus sign
# # which makes the AVS scale go positive up
# sec_axis(
# ~ -. + refelectrodes::as.SHE(0, scale = "AVS"),
# name = "E(AVS)/V")) +
# # a more suitable theme
# theme_classic() +
# # completely remove the x-axis
# theme(
# axis.text.x = element_blank(),
# axis.title.x = element_blank(),
# axis.line.x = element_blank(),
# axis.ticks.x = element_blank())
## ----'bandgaps-tikz', results='asis'----------------------------------------------
# this chunk is bit of a hack to tie together the TikZ code with the bandgaps dataset
tikz_materials <-
bandgaps::semiconductors %>%
# exclude a few to make the TikZ plot fit (the TikZ plot dimensions are not set dynamically, that's something to do)
filter(!formula %in% c("CdSe", "MoS2", "PbS")) %>%
select(CB, VB, Eg, formula, polymorph) %>%
mutate(CB = paste0("\\drawbg{", prettyNum(CB))) %>%
# fnsymb column is empty since we only show oxides
# so we will hack together an empty column in the right place
mutate(Eg = paste(Eg, "\\phantom{1}")) %>%
separate(Eg, sep = " ", c("Eg", "fnsymb")) %>%
mutate(polymorph = paste0(polymorph, "}"))
tikz_materials %>% write.table(
row.names = F,
col.names = F,
sep = "} {",
quote = F)
## ----'gitR-info', echo=FALSE, results='markup', cache=FALSE-----------------------
# status(repo)
## ----'R-session-info', echo=FALSE, results='asis', cache=FALSE--------------------
toLatex(sessionInfo(), locale=F)
## ----'pdflatex-version', echo=FALSE, results='asis'-------------------------------
latex.version.text <- system(command = "pdflatex -version", intern = TRUE)
# quick fixes: replace "\o" with "o", and remove all empty rows in latex.version.text
cat(paste0("\\noindent\n", paste(sub("\\\\o", "o", latex.version.text[which(latex.version.text != "")]), collapse = "\\\\\n")))
solarchemist/bandgaps documentation built on July 9, 2023, 3:59 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
## ----'R-setup', echo=F, results='hide', cache=FALSE-------------------------------
options(
tikzDefaultEngine = "pdftex",
"tikzLatexPackages" = c(
"\\usepackage{tikz}\n",
"\\usepackage[active,tightpage,psfixbb]{preview}\n",
"\\PreviewEnvironment{pgfpicture}\n",
"\\setlength\\PreviewBorder{0pt}\n",
"\\usepackage{chemformula}\n",
"\\setchemformula{charge-style=math}\n",
"\\usepackage{siunitx}\n",
"\\sisetup{separate-uncertainty,detect-family,range-phrase=\\ensuremath{\\text{ to }}}\n",
"\\DeclareSIUnit{\\counts}{cts}\n",
"\\DeclareSIUnit{\\cps}{cps}\n",
"\\DeclareSIUnit{\\molar}{\\mole\\per\\cubic\\deci\\metre}\n",
"\\DeclareSIUnit{\\Molar}{\\textsc{m}}\n",
"\\DeclareSIUnit{\\vsAgCl}{vs~\\ch{Ag}/\\ch{AgCl}}",
"\\DeclareSIUnit{\\vsNHE}{vs~NHE}",
"\\DeclareSIUnit{\\vsSHE}{vs~SHE}",
"\\DeclareSIUnit{\\vsSCE}{vs~SCE}",
"\\DeclareSIUnit{\\voltAgCl}{\\volt\\vsAgCl}",
"\\DeclareSIUnit{\\voltNHE}{\\volt\\vsNHE}",
"\\DeclareSIUnit{\\voltSHE}{\\volt\\vsSHE}",
"\\DeclareSIUnit{\\voltSCE}{\\volt\\vsSCE}"),
digits = 7,
width = 84,
continue = " ",
prompt = "> ",
stringsAsFactors = FALSE)
# here::i_am("vignettes/diagram.Rnw")
## ----'load-R-packages', echo=F, results='hide', message=FALSE---------------------
library(bandgaps)
# packages listed below should also be listed in DESCRIPTION
library(common)
# library(here)
# library(git2r)
# repo <- repository(here())
library(graphics)
library(ggplot2)
# library(ggrepel) # am I using it?
library(dplyr)
library(tidyr)
library(xtable)
library(knitr)
opts_knit$set(
self.contained = FALSE,
child.path = '')
opts_chunk$set(
dev = 'tikz',
# external = TRUE only takes effect when tikz is the ONLY dev option
external = TRUE,
cache = FALSE,
fig.width = 3.40, # 2.60,
# corresponding height based on golden ratio (1.618034):
# W 3.54 ==> H 2.19 >> works better >> W 2.60, H 1.61
# W 5.51 ==> H 3.41
# W 7.48 ==> H 4.62 >> works better >> W 5.40, H 3.34
fig.height = 2.10, # 1.61,
out.width = '3.40in', # '2.60in',
fig.align = 'center',
# size affects all knitr output. We use it primarily
# to match knitr font size to figure captions
size = 'footnotesize',
echo = FALSE,
eval = TRUE,
results = 'hide',
message = FALSE,
tidy = FALSE)
## ----ref.label='bandgaps-plot-figure', echo=TRUE, eval=FALSE----------------------
# plot_bandgaps(bandgaps::semiconductors %>% filter(Nernstian == TRUE))
## ----'bandgaps-plot-figure', fig.width=6, fig.height=3.71, out.width='6in'--------
plot_bandgaps(bandgaps::semiconductors %>% filter(Nernstian == TRUE))
## ----'bandgaps-ggplot-figure', fig.width=6, fig.height=3.71, out.width='6in'------
ggplot_materials <-
bandgaps::semiconductors %>%
# for recalculation of pH, only display Nernstian semiconductors
filter(class == "oxide")
ggplot_materials <-
ggplot_materials %>%
# add column with x variable
# NOTE: do this as the last step to avoid weird visual gaps
# 0.4 is the x-value of the first line, stepsize 1.0
mutate(x = seq(0.4, dim(ggplot_materials)[1], by = 1.0))
ggplot(data = ggplot_materials) +
# water redox lines
geom_hline(yintercept = 0.00, colour = "red", linetype = "dashed", size = 0.3) +
geom_hline(yintercept = 1.23, colour = "blue", linetype = "dashed", size = 0.3) +
# band gaps visualised as vertical lines
geom_linerange(
aes(x = x, ymin = CB, ymax = VB),
size = 0.8) +
# label each compound
geom_text(
aes(
x = x,
label = paste0("\\ch{", formula, "}"),
# can we put the label at VB if CB > than some value?
# also add a constant space between CB/VB and label
y = ifelse(CB > -0.5, CB - 0.05, VB + 0.05),
# left-adjust labels at CB, and right-adjust labels at VB
hjust = ifelse(CB > -0.5, 0, 1)),
size = 3,
vjust = 0.5,
angle = 80) +
# flip primary y-axis and create secondary AVS axis
scale_y_continuous(
name = "E(SHE)/V",
# make sure each unit step is marked
breaks = seq(-4, 6),
# expand() parameters are
# a multiplicative and an absolute expansion
# we add some space to make sure the labels of the largest Eg fits
expand = c(0, 0.65),
trans = "reverse",
sec.axis =
# note the initial minus sign
# which makes the AVS scale go positive up
sec_axis(
~ -. + refelectrodes::as.SHE(0, scale = "AVS"),
name = "E(AVS)/V")) +
# a more suitable theme
theme_classic() +
# completely remove the x-axis
theme(
axis.text.x = element_blank(),
axis.title.x = element_blank(),
axis.line.x = element_blank(),
axis.ticks.x = element_blank())
## ----ref.label='bandgaps-ggplot-figure', echo=TRUE, eval=FALSE--------------------
# ggplot_materials <-
# bandgaps::semiconductors %>%
# # for recalculation of pH, only display Nernstian semiconductors
# filter(class == "oxide")
# ggplot_materials <-
# ggplot_materials %>%
# # add column with x variable
# # NOTE: do this as the last step to avoid weird visual gaps
# # 0.4 is the x-value of the first line, stepsize 1.0
# mutate(x = seq(0.4, dim(ggplot_materials)[1], by = 1.0))
# ggplot(data = ggplot_materials) +
# # water redox lines
# geom_hline(yintercept = 0.00, colour = "red", linetype = "dashed", size = 0.3) +
# geom_hline(yintercept = 1.23, colour = "blue", linetype = "dashed", size = 0.3) +
# # band gaps visualised as vertical lines
# geom_linerange(
# aes(x = x, ymin = CB, ymax = VB),
# size = 0.8) +
# # label each compound
# geom_text(
# aes(
# x = x,
# label = paste0("\\ch{", formula, "}"),
# # can we put the label at VB if CB > than some value?
# # also add a constant space between CB/VB and label
# y = ifelse(CB > -0.5, CB - 0.05, VB + 0.05),
# # left-adjust labels at CB, and right-adjust labels at VB
# hjust = ifelse(CB > -0.5, 0, 1)),
# size = 3,
# vjust = 0.5,
# angle = 80) +
# # flip primary y-axis and create secondary AVS axis
# scale_y_continuous(
# name = "E(SHE)/V",
# # make sure each unit step is marked
# breaks = seq(-4, 6),
# # expand() parameters are
# # a multiplicative and an absolute expansion
# # we add some space to make sure the labels of the largest Eg fits
# expand = c(0, 0.65),
# trans = "reverse",
# sec.axis =
# # note the initial minus sign
# # which makes the AVS scale go positive up
# sec_axis(
# ~ -. + refelectrodes::as.SHE(0, scale = "AVS"),
# name = "E(AVS)/V")) +
# # a more suitable theme
# theme_classic() +
# # completely remove the x-axis
# theme(
# axis.text.x = element_blank(),
# axis.title.x = element_blank(),
# axis.line.x = element_blank(),
# axis.ticks.x = element_blank())
## ----'bandgaps-tikz', results='asis'----------------------------------------------
# this chunk is bit of a hack to tie together the TikZ code with the bandgaps dataset
tikz_materials <-
bandgaps::semiconductors %>%
# exclude a few to make the TikZ plot fit (the TikZ plot dimensions are not set dynamically, that's something to do)
filter(!formula %in% c("CdSe", "MoS2", "PbS")) %>%
select(CB, VB, Eg, formula, polymorph) %>%
mutate(CB = paste0("\\drawbg{", prettyNum(CB))) %>%
# fnsymb column is empty since we only show oxides
# so we will hack together an empty column in the right place
mutate(Eg = paste(Eg, "\\phantom{1}")) %>%
separate(Eg, sep = " ", c("Eg", "fnsymb")) %>%
mutate(polymorph = paste0(polymorph, "}"))
tikz_materials %>% write.table(
row.names = F,
col.names = F,
sep = "} {",
quote = F)
## ----'gitR-info', echo=FALSE, results='markup', cache=FALSE-----------------------
# status(repo)
## ----'R-session-info', echo=FALSE, results='asis', cache=FALSE--------------------
toLatex(sessionInfo(), locale=F)
## ----'pdflatex-version', echo=FALSE, results='asis'-------------------------------
latex.version.text <- system(command = "pdflatex -version", intern = TRUE)
# quick fixes: replace "\o" with "o", and remove all empty rows in latex.version.text
cat(paste0("\\noindent\n", paste(sub("\\\\o", "o", latex.version.text[which(latex.version.text != "")]), collapse = "\\\\\n")))
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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