Community Assembly Mechanisms by iCAMP

[TongZhou2017]

DOI: 10.1016/j.envpol.2022.120243
Status: ask for tree and template files
Location: Fig3A, FigS4
Elements:
Fig3A

Fig4A

10.1016j.envpol.2022.120243(2).zip

[TongZhou2017]

Fig3 left

library(itol.toolkit)
library(data.table)

tree_1 <- "~/Downloads/itol.annotation-package.output/10.1016j.envpol.2022.120243/Fig.3/Abundant-tree/abunt-tree.nwk"
hub_1 <- create_hub(tree_1)
data_file_1 <- "~/Downloads/itol.annotation-package.output/10.1016j.envpol.2022.120243/Fig.3/Abundant-tree/metadata.txt"
data_1 <- data.table::fread(data_file_1)

# relabel by genus
unit_1 <- create_unit(data = data_1 %>% select(ID, Genus), 
                      key = "rep_Zheng2022ep_3al_1_labels", 
                      type = "LABELS",
                      tree = tree_1)

# tree_colors range by phylum
unit_2 <- create_unit(data = data_1 %>% select(ID, Phylum), 
                    key = "rep_Zheng2022ep_3al_2_range", 
                    type = "TREE_COLORS", 
                    subtype = "range", 
                    tree = tree_1)

# color_strip by class
set.seed(123)
unit_3 <- create_unit(data = data_1 %>% select(ID, Class), 
                      key = "rep_Zheng2022ep_3al_3_strip",
                      type = "DATASET_COLORSTRIP",
                      color = "wesanderson",
                      tree = tree_1)
unit_3@common_themes$basic_theme$margin <- 50

# simple_bar by NS
unit_4 <- create_unit(data = data_1 %>% select(ID, NS), 
                      key = "rep_Zheng2022ep_3al_4_simplebar", 
                      type = "DATASET_SIMPLEBAR",
                      tree = tree_1)
unit_4@specific_themes$basic_plot$size_max <- 100

# simple_bar by OS
unit_5 <- create_unit(data = data_1 %>% select(ID, OS), 
                      key = "rep_Zheng2022ep_3al_5_simplebar", 
                      type = "DATASET_SIMPLEBAR",
                      tree = tree_1)
unit_5@specific_themes$basic_plot$size_max <- 100

# simple_bar by OS
unit_6 <- create_unit(data = data_1 %>% select(ID, Dissimilarity), 
                      key = "rep_Zheng2022ep_3al_6_gradient", 
                      type = "DATASET_GRADIENT", 
                      tree = tree_1)
#unit_6@specific_themes$heatmap$color$min <- "#0000ff"
#unit_6@specific_themes$heatmap$color$max <- "#ff0000"
hub_1 <- hub_1 + 
  unit_1 + 
  unit_2 + 
  unit_3 + 
  unit_4 + 
  unit_5 + 
  unit_6
write_hub(hub_1,getwd())

Fig3 right

tree_2 <- "~/Downloads/itol.annotation-package.output/10.1016j.envpol.2022.120243/Fig.3/Rare-tree/rare-tree.nwk"
hub_2 <- create_hub(tree_2)
data_file_2 <- "~/Downloads/itol.annotation-package.output/10.1016j.envpol.2022.120243/Fig.3/Rare-tree/metadata.txt"
data_2 <- data.table::fread(data_file_2)

# relabel by genus
unit_7 <- create_unit(data = data_2 %>% select(ID, Genus), 
                      key = "rep_Zheng2022ep_3ar_1_labels", 
                      type = "LABELS",
                      tree = tree_2)

# tree_colors range by phylum
unit_8 <- create_unit(data = data_2 %>% select(ID, Phylum), 
                    key = "rep_Zheng2022ep_3ar_2_range", 
                    type = "TREE_COLORS", 
                    subtype = "range", 
                    tree = tree_2)

# color_strip by class
set.seed(123)
unit_9 <- create_unit(data = data_2 %>% select(ID, Class), 
                      key = "rep_Zheng2022ep_3ar_3_strip",
                      type = "DATASET_COLORSTRIP",
                      color = "wesanderson",
                      tree = tree_2)
unit_9@common_themes$basic_theme$margin <- 50

# simple_bar by NS
unit_10 <- create_unit(data = data_2 %>% select(ID, NS), 
                      key = "rep_Zheng2022ep_3ar_4_simplebar", 
                      type = "DATASET_SIMPLEBAR",
                      tree = tree_2)
unit_10@specific_themes$basic_plot$size_max <- 100

# simple_bar by OS
unit_11 <- create_unit(data = data_2 %>% select(ID, OS), 
                      key = "rep_Zheng2022ep_3ar_5_simplebar", 
                      type = "DATASET_SIMPLEBAR",
                      tree = tree_2)
unit_11@specific_themes$basic_plot$size_max <- 100

# simple_bar by OS
unit_12 <- create_unit(data = data_2 %>% select(ID, Dissimilarity), 
                      key = "rep_Zheng2022ep_3ar_6_gradient", 
                      type = "DATASET_GRADIENT", 
                      tree = tree_2)
#unit_6@specific_themes$heatmap$color$min <- "#0000ff"
#unit_6@specific_themes$heatmap$color$max <- "#ff0000"
hub_2 <- hub_2 + 
  unit_7 + 
  unit_8 + 
  unit_9 + 
  unit_10 + 
  unit_11 + 
  unit_12
write_hub(hub_2,getwd())

Fig4

tree_3 <- "~/Downloads/itol.annotation-package.output/10.1016j.envpol.2022.120243/Fig.4/assemblytree.nwk"
hub_3 <- create_hub(tree_3)
data_file_3 <- "~/Downloads/itol.annotation-package.output/10.1016j.envpol.2022.120243/Fig.4/metadata.txt"
data_3 <- data.table::fread(data_file_3)

# tree_colors range by phylum
unit_13 <- create_unit(data = data_3 %>% select(ID, Phylum), 
                    key = "rep_Zheng2022ep_4a_1_range", 
                    type = "TREE_COLORS", 
                    subtype = "range", 
                    tree = tree_3)
write_unit(unit_13,
           paste0(getwd(),"/rep_Zheng2022ep_4a_2_range.txt"))

top_10_NS <- data_3 %>% select(ID,`NS-bar`) %>% arrange(desc(`NS-bar`)) %>% head(n=10) %>% pull(ID)
top_10_OS <- data_3 %>% select(ID,`OS-bar`) %>% arrange(desc(`OS-bar`)) %>% head(n=10) %>% pull(ID)
RA_1 <- data_3 %>% mutate(pct = `OS-bar`+`NS-bar`/sum(data_3$`OS-bar`,data_3$`NS-bar`)) %>% select(ID, pct) %>% arrange(pct) %>% filter(pct > 1) %>% pull(ID)
RA_ids <- unique(c(top_10_NS,top_10_OS,RA_1))
df_text <- data.frame(id = RA_ids, text = rep("#",length(RA_ids)))
unit_14 <- create_unit(data = df_text, 
                       key = "rep_Zheng2022ep_4a_3_text", 
                       type = "DATASET_TEXT",
                       size_factor = 1,
                       position = 0.9,
                       rotation=0,
                       color = "#000000",
                       tree = tree_3)
write_unit(unit_14,
           paste0(getwd(),"/rep_Zheng2022ep_4a_3_text.txt"))

df_cap_NS <- data_3 %>% select(ID, starts_with("NS"))
df_bar_NS <- df_cap_NS %>% select(ID,ends_with("bar"))
df_cap_NS <- df_cap_NS %>% select(-ends_with("bar"))
unit_15 <- create_unit(data = df_cap_NS, 
                       key = "rep_Zheng2022ep_4a_4_heatmap",
                       type = "DATASET_HEATMAP", 
                       tree = tree_3)
write_unit(unit_15,
           paste0(getwd(),"/rep_Zheng2022ep_4a_4_heatmap.txt"))

# simple_bar by OS
df_bar_NS$`NS-bar` <- round(df_bar_NS$`NS-bar`,3)
unit_16 <- create_unit(data = df_bar_NS, 
                      key = "rep_Zheng2022ep_4a_6_simplebar", 
                      type = "DATASET_SIMPLEBAR",
                      tree = tree_3)
unit_16@specific_themes$basic_plot$size_max <- 100
write_unit(unit_16,
           paste0(getwd(),"/rep_Zheng2022ep_4a_6_simplebar.txt"))

df_cap_OS <- data_3 %>% select(ID, starts_with("OS"))
df_bar_OS <- df_cap_OS %>% select(ID,ends_with("bar"))
df_cap_OS <- df_cap_OS %>% select(-ends_with("bar"))
unit_17 <- create_unit(data = df_cap_OS, 
                       key = "rep_Zheng2022ep_4a_7_heatmap",
                       type = "DATASET_HEATMAP", 
                       tree = tree_3)
write_unit(unit_17,
           paste0(getwd(),"/rep_Zheng2022ep_4a_7_heatmap.txt"))

# simple_bar by OS
df_bar_OS$`OS-bar` <- round(df_bar_OS$`OS-bar`,3)
unit_18 <- create_unit(data = df_bar_OS, 
                      key = "rep_Zheng2022ep_4a_8_simplebar", 
                      type = "DATASET_SIMPLEBAR",
                      tree = tree_3)
unit_18@specific_themes$basic_plot$size_max <- 100
write_unit(unit_18,
           paste0(getwd(),"/rep_Zheng2022ep_4a_8_simplebar.txt"))