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Kodutöö4_klaster.Rmd
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---
title: "Klasteanalüüsi kodutöö"
author: "Siim"
date: "4/4/2021"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
```{r}
library(essurvey)
library(tidyverse)
library(pheatmap)
library(ggplot2)
library(RColorBrewer)
library(rnaturalearth)
library(sf)
```
```{r}
set_email("[email protected]")
eu9 <- import_rounds(9, format="spss")
eu9 <- eu9 %>%
select(cntry, freehms, hmsfmlsh, hmsacld, pspwght)
#Teeme võrdleva ploti toorestest vastustest
cntry_raw_plt <- eu9 %>%
pivot_longer(cols = c("freehms", "hmsfmlsh", "hmsacld"), names_to = "Question", values_to = "Answer") %>%
ggplot(aes(x=cntry, fill = as.factor(Answer))) +
geom_bar(position="fill") +
coord_flip()+
xlab("Riik")+
ylab("Osakaal")+
scale_fill_manual(name = "Vastus",
labels = c("1-Agree strongly", "2-Agree", "3-Neither agree nor disagree", "4-Disagree", "5-Disagree strongly"),
values = c("darkgreen", "lightgreen", "#F7F7F7", "#CC99FF", "#8E0152"),
na.value = "gray20")+
facet_wrap(~Question, labeller = labeller(Question = c(`freehms`="Gays and lesbians free \n to live life as they wish",
`hmsfmlsh`="Ashamed if close family \n member gay or lesbian",
`hmsacld`="Gay and lesbian couples right \n to adopt children")))+
theme(strip.text.x = element_text( size = 6, color = "black", face = "bold.italic"))+
theme(axis.text.x = element_text(angle = 45))
ggsave("agg_cluster_plot2.png", cntry_raw_plt, device = "png", height = 12, width = 20, units = c("cm"))
#Võtame kaalutud keskmise
eu9_agg <- eu9 %>%
group_by(cntry) %>%
summarise(freehms_mean = weighted.mean(as.numeric(freehms), na.rm=T, w = pspwght),
hmsfmlsh_mean = weighted.mean(as.numeric(hmsfmlsh), na.rm=T, w = pspwght),
hmsacld_mean = weighted.mean(as.numeric(hmsacld), na.rm=T, w = pspwght))
eu9_agg_scaled <-eu9_agg %>%
mutate(freehms_mean = scale(freehms_mean),
hmsfmlsh_mean = scale(hmsfmlsh_mean),
hmsacld_mean = scale(hmsacld_mean))
cbind(eu9_agg, eu9_agg_scaled)
```
```{r}
#Plot keskmistest
agg_plot <-eu9_agg %>%
pivot_longer(cols = c("freehms_mean", "hmsfmlsh_mean", "hmsacld_mean"), names_to = "Question", values_to = "Mean score") %>%
ggplot(aes(x=cntry, y = `Mean score`, color = Question, group = Question)) +
geom_point()+
geom_line()+
xlab("Riik")+
ylab("Keskmine skoor")+
scale_color_brewer(name = "Küsimus",
labels = c("Gays and lesbians free \n to live life as they wish",
"Ashamed if close family \n member gay or lesbian",
"Gay and lesbian couples right \n to adopt children"),
palette="Dark2")+
theme(legend.position = "top") +
annotate("text", x = 1, y = 4.8,
label = "Keskmine põhineb skaalal: \n 1 - Agree Strongly \n 5 - Disagree strongly",
hjust = 0)
ggsave("agg_cluster_plot_1.png", agg_plot, device = "png", height = 9, width = 10)
```
```{r}
eu9_agg_rows <- eu9_agg$cntry
eu9_agg_rows
agg_mat <- eu9_agg %>%
select(freehms_mean, hmsfmlsh_mean, hmsacld_mean) %>%
as.matrix()
eu9_rows <- data.frame(Question = factor(c("Gays and lesbians free to live life as they wish",
"Ashamed if close family member gay or lesbian",
"Gay and lesbian couples right to adopt children")))
rownames(eu9_rows) <- colnames(agg_mat)
rownames(agg_mat) <- eu9_agg_rows
d_agg <- stats::dist(agg_mat)
d_agg_comp <- hclust(d_agg, method = "complete")
clusters <- as.data.frame(cutree(d_agg_comp, 4)) %>%
rownames_to_column() %>%
rename(iso_a2 = rowname, cluster = `cutree(d_agg_comp, 4)`)
col_anns <- as.data.frame(cutree(d_agg_comp, 4)) %>%
rename(Cluster = `cutree(d_agg_comp, 4)`) %>%
mutate(Cluster = as.character(Cluster))
```
```{r}
#Kõige paremini klasterdas complete, sest teised küll andsid ka selgelt kaks erinevat klastrit, aga vähem selgelt olid eristatavad 4 tk.
comp_heat <- pheatmap(t(agg_mat),
main = "ESS heatmap",
show_rownames = F,
show_colnames = T,
cluster_rows = F,
clustering_distance_col = "euclidean",
clustering_method = "complete",
angle_col = 45,
fontsize_number = 7,
number_color = "black",
cutree_cols = 4,
cellheight = 35,
cellwidth = 16,
annotation_row = eu9_rows,
annotation_col = col_anns,
legend_breaks = c(-2, 4.5),
legend_labels = c("Agree strongly","Disagree strongly"),
color = colorRampPalette(c("darkgreen", "#F7F7F7", "#8E0152"))(99),
annotation_colors = list(Question = c(`Gays and lesbians free to live life as they wish` = "#1B9E77",
`Ashamed if close family member gay or lesbian` = "#D95F02",
`Gay and lesbian couples right to adopt children` = "#7570B3"),
Cluster = c(`1` = "#E31A1C",
`2` = "#6A3D9A",
`3` = "#CAB2D6",
`4` = "#FB9A99")),
filename = "Ess_heat1_2.png",
height = 9,
width = 15.5)
pheatmap(t(agg_mat),
main = "ESS heatmap",
show_rownames = F,
show_colnames = T,
cluster_rows = F,
clustering_distance_col = "euclidean",
clustering_method = "single",
angle_col = 45,
display_numbers = T,
fontsize_number = 7,
number_color = "black",
cutree_cols = 2,
cellheight = 35,
cellwidth = 16,
annotation_row = eu9_rows,
legend_breaks = c(1.5, 4.5),
legend_labels = c("Agree strongly","Disagree strongly"),
color = colorRampPalette(c("darkgreen", "#F7F7F7", "#8E0152"))(99),
filename = "Ess_heat2_2.png",
height = 9,
width = 15.5)
pheatmap(t(agg_mat),
main = "ESS heatmap",
show_rownames = F,
show_colnames = T,
cluster_rows = F,
clustering_distance_col = "euclidean",
clustering_method = "ward.D2",
angle_col = 45,
display_numbers = T,
fontsize_number = 7,
number_color = "black",
cutree_cols = 4,
cellheight = 35,
cellwidth = 16,
annotation_row = eu9_rows,
annotation_col = col_anns,
legend_breaks = c(1.5, 4.5),
legend_labels = c("Agree strongly","Disagree strongly"),
color = colorRampPalette(c("darkgreen", "#F7F7F7", "#8E0152"))(99),
annotation_colors = list(Question = c(`Gays and lesbians free to live life as they wish` = "#1B9E77",
`Ashamed if close family member gay or lesbian` = "#D95F02",
`Gay and lesbian couples right to adopt children` = "#7570B3"),
Cluster = c(`1` = "#E31A1C",
`2` = "#6A3D9A",
`3` = "#CAB2D6",
`4` = "#FB9A99")),
filename = "Ess_heat3_2.png",
height = 9,
width = 15.5)
pheatmap(t(agg_mat),
main = "ESS heatmap",
show_rownames = F,
show_colnames = T,
cluster_rows = F,
clustering_distance_col = "euclidean",
clustering_method = "average",
angle_col = 45,
display_numbers = T,
fontsize_number = 7,
number_color = "black",
cutree_cols = 2,
cellheight = 35,
cellwidth = 16,
legend_breaks = c(1.5, 4.5),
legend_labels = c("Agree strongly","Disagree strongly"),
annotation_row = eu9_rows,
color = colorRampPalette(c("darkgreen", "#F7F7F7", "#8E0152"))(99),
annotation_colors = list(Question = c(`Gays and lesbians free to live life as they wish` = "#1B9E77",
`Ashamed if close family member gay or lesbian` = "#D95F02",
`Gay and lesbian couples right to adopt children` = "#7570B3")),
filename = "Ess_heat4_2.png",
height = 9,
width = 15.5)
```
```{r}
europeanUnion <- c("Austria","Belgium","Bulgaria","Croatia","Cyprus",
"Czech Rep.","Denmark","Estonia","Finland","France",
"Germany","Greece","Hungary","Ireland","Italy","Latvia",
"Lithuania","Luxembourg","Malta","Netherlands","Poland",
"Portugal","Romania","Slovakia","Slovenia","Spain",
"Sweden")
world_map <- ne_countries(scale = 50, returnclass = 'sf')
europe_map <- world_map %>% filter(name %in% europeanUnion)
europe_bbox <- st_bbox(c(xmin = -12, xmax = 34, ymax = 71, ymin = 34), crs = st_crs(4326))
europe_map <- europe_map %>%
st_crop(europe_bbox)
cluster_map <- europe_map %>%
right_join(clusters) %>%
mutate(cluster = as.factor(cluster)) %>%
ggplot() +
geom_sf(aes(fill = factor(cluster))) +
theme_void()+
scale_fill_manual(values = c("#E31A1C", "#6A3D9A", "#CAB2D6", "#FB9A99"), name = "Cluster")
cluster_map2 <- europe_map %>%
right_join(clusters) %>%
mutate(cluster = as.factor(cluster)) %>%
ggplot() +
geom_sf(aes(fill = factor(cluster))) +
theme_void()+
scale_fill_manual(values = c("#E31A1C", "#6A3D9A", "#CAB2D6", "#FB9A99"), name = "Cluster")
cluster_map
ggsave("cluster_map2.png", cluster_map)
```