Figure_2A
ZZ, APB, TFJ
2023-12-20
Last updated: 2023-12-20
Checks: 7 0
Knit directory:
workflowr-policy-landscape/
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Creating Figure 2A
Figure 2A shows gamma values (x-axis, means ± sd) that are the strength of association between a set of stakeholder documents (y-axis) and the corresponding topic.
High gamma values are strong associations.
We plotted the values for four main topics (side labels): Open Research (green), Community and Support (red), Innovation and Solutions (yellow) and Publication Process (blue).
The data for this are produced in 2_Topic_modeling
R Setup and packages
rm(list=ls())Libraries
library(tidyverse)── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ──
✔ dplyr 1.1.3 ✔ readr 2.1.4
✔ forcats 1.0.0 ✔ stringr 1.5.0
✔ ggplot2 3.4.3 ✔ tibble 3.2.1
✔ lubridate 1.9.3 ✔ tidyr 1.3.0
✔ purrr 1.0.2
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag() masks stats::lag()
ℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errorslibrary(dplyr)
library(ggplot2)Import data to create Figure 2A
The data are produced in 2_Topic_modeling
# Importing data produced in "2_Topic_modeling.Rmd"
# df_doc_level_stm_gamma <- read_csv(file = "./output/created_datasets/df_doc_level_stm_gamma.csv")
# Importing data that we originally created and used in our analysis
df_doc_level_stm_gamma <- read.csv(file = "./data/original_dataset_reproducibility_check/original_df_doc_level_stm_gamma.csv")Data management
# glimpse(df_doc_level_stm_gamma)
# head(df_doc_level_stm_gamma, 10)
df_figure1_gamma <- df_doc_level_stm_gamma %>%
select(-total_topic, -total_sent)
df_figure1_gamma$prop <- df_figure1_gamma$prop *100
df_figure1_gamma_wide <- df_figure1_gamma %>%
spread(topic, prop) %>%
rename(topic_1 = `1`, topic_2 = `2`, topic_3 = `3`, topic_4 = `4`)
# Topic/Category 1: Open Research
# Topic/Category 2: Community & Support
# Topic/Category 3: Innovation & Solution
# Topic/Category 4: Publication process (control)
df_figure1_gamma_wide2 = data.frame(
document = rep(df_figure1_gamma_wide$name,4),
stakeholder = rep(df_figure1_gamma_wide$stakeholder,4),
# type = c(rep("Topic 1",129), rep("Topic 2",129), rep("Topic 3",129), rep("Topic 4", 129)),
type = c(rep("1. Open Research",129), rep("2. Community and Support",129), rep("3. Innovation and Solutions",129), rep("4. Publication Process", 129)),
perc = c(df_figure1_gamma_wide$topic_1, df_figure1_gamma_wide$topic_2, df_figure1_gamma_wide$topic_3, df_figure1_gamma_wide$topic_4),
perc2 = c(df_figure1_gamma_wide$topic_1, df_figure1_gamma_wide$topic_2, df_figure1_gamma_wide$topic_3, df_figure1_gamma_wide$topic_4)
)
# adding quantiles values
sum_figure1_gamma_wide2 =
df_figure1_gamma_wide2 %>%
group_by(stakeholder, type) %>%
dplyr::summarize(lower = quantile(perc, probs = .25), upper = quantile(perc, probs = .75), perc_fin = mean(perc)) %>%
rename(perc = perc_fin)`summarise()` has grouped output by 'stakeholder'. You can override using the
`.groups` argument.Graph production
figure_topics <- ggplot() +
geom_point(data = df_figure1_gamma_wide2, aes(x = perc, y = stakeholder, colour = type), alpha = 0.2, position = position_jitter(), show.legend = FALSE) +
geom_pointrange(data = sum_figure1_gamma_wide2, aes(x = perc, xmin = lower, xmax = upper, y = stakeholder, colour = type), show.legend = FALSE) +
facet_grid(.~type) +
labs(x = "Topics occuring in documents (%) gamma", y = "") +
scale_color_manual(values = c("dark green", "dark red", "darkgoldenrod", "dark blue")) +
theme_classic()
figure_topics
# # UNCOMMENT TO SAVE FIGURES
# figure_name <- paste0("./output/Figure_2A/Figure_2A.png")
# png(file=figure_name,
# width= 3000, height= 2000, res=400)
# figure_topics
# dev.off()Session information
sessionInfo()R version 4.3.1 (2023-06-16)
Platform: x86_64-apple-darwin20 (64-bit)
Running under: macOS Monterey 12.6
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: Europe/London
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] lubridate_1.9.3 forcats_1.0.0 stringr_1.5.0 dplyr_1.1.3
[5] purrr_1.0.2 readr_2.1.4 tidyr_1.3.0 tibble_3.2.1
[9] ggplot2_3.4.3 tidyverse_2.0.0 workflowr_1.7.1
loaded via a namespace (and not attached):
[1] sass_0.4.7 utf8_1.2.3 generics_0.1.3 stringi_1.7.12
[5] hms_1.1.3 digest_0.6.33 magrittr_2.0.3 timechange_0.2.0
[9] evaluate_0.21 grid_4.3.1 fastmap_1.1.1 rprojroot_2.0.3
[13] jsonlite_1.8.7 processx_3.8.2 whisker_0.4.1 ps_1.7.5
[17] promises_1.2.1 httr_1.4.7 fansi_1.0.4 scales_1.2.1
[21] jquerylib_0.1.4 cli_3.6.1 rlang_1.1.1 munsell_0.5.0
[25] withr_2.5.1 cachem_1.0.8 yaml_2.3.7 tools_4.3.1
[29] tzdb_0.4.0 colorspace_2.1-0 httpuv_1.6.11 vctrs_0.6.3
[33] R6_2.5.1 lifecycle_1.0.3 git2r_0.32.0 fs_1.6.3
[37] pkgconfig_2.0.3 callr_3.7.3 pillar_1.9.0 bslib_0.5.1
[41] later_1.3.1 gtable_0.3.4 glue_1.6.2 Rcpp_1.0.11
[45] xfun_0.40 tidyselect_1.2.0 rstudioapi_0.15.0 knitr_1.44
[49] farver_2.1.1 htmltools_0.5.6 labeling_0.4.3 rmarkdown_2.25
[53] compiler_4.3.1 getPass_0.2-2
sessionInfo()R version 4.3.1 (2023-06-16)
Platform: x86_64-apple-darwin20 (64-bit)
Running under: macOS Monterey 12.6
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: Europe/London
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] lubridate_1.9.3 forcats_1.0.0 stringr_1.5.0 dplyr_1.1.3
[5] purrr_1.0.2 readr_2.1.4 tidyr_1.3.0 tibble_3.2.1
[9] ggplot2_3.4.3 tidyverse_2.0.0 workflowr_1.7.1
loaded via a namespace (and not attached):
[1] sass_0.4.7 utf8_1.2.3 generics_0.1.3 stringi_1.7.12
[5] hms_1.1.3 digest_0.6.33 magrittr_2.0.3 timechange_0.2.0
[9] evaluate_0.21 grid_4.3.1 fastmap_1.1.1 rprojroot_2.0.3
[13] jsonlite_1.8.7 processx_3.8.2 whisker_0.4.1 ps_1.7.5
[17] promises_1.2.1 httr_1.4.7 fansi_1.0.4 scales_1.2.1
[21] jquerylib_0.1.4 cli_3.6.1 rlang_1.1.1 munsell_0.5.0
[25] withr_2.5.1 cachem_1.0.8 yaml_2.3.7 tools_4.3.1
[29] tzdb_0.4.0 colorspace_2.1-0 httpuv_1.6.11 vctrs_0.6.3
[33] R6_2.5.1 lifecycle_1.0.3 git2r_0.32.0 fs_1.6.3
[37] pkgconfig_2.0.3 callr_3.7.3 pillar_1.9.0 bslib_0.5.1
[41] later_1.3.1 gtable_0.3.4 glue_1.6.2 Rcpp_1.0.11
[45] xfun_0.40 tidyselect_1.2.0 rstudioapi_0.15.0 knitr_1.44
[49] farver_2.1.1 htmltools_0.5.6 labeling_0.4.3 rmarkdown_2.25
[53] compiler_4.3.1 getPass_0.2-2