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romanhaa/alluvial.R

Last active February 13, 2020 17:37
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Revisions

  1. romanhaa revised this gist Feb 13, 2020. 1 changed file with 16 additions and 1 deletion.
    17 changes: 16 additions & 1 deletion alluvial.R
    View file
    Original file line number Diff line number Diff line change
    @@ -68,4 +68,19 @@ p <- ggplot(
    )
    ) +
    geom_alluvium(aes(fill = stratum)) +
    geom_stratum(aes(fill = stratum))
    geom_stratum(aes(fill = stratum)) +
    geom_label(stat = "stratum") +
    theme_bw() +
    labs(x = "", y = "") +
    theme_bw() +
    theme(
    legend.position = "none",
    axis.title = element_blank(),
    axis.text.x = element_text(face = "bold", colour = "black", size=15),
    axis.text.y = element_blank(),
    axis.ticks.y = element_blank(),
    panel.grid.major = element_blank(),
    panel.grid.minor = element_blank(),
    panel.border = element_blank(),
    axis.ticks.x = element_blank()
    )
  2. romanhaa revised this gist Feb 13, 2020. 1 changed file with 21 additions and 5 deletions.
    26 changes: 21 additions & 5 deletions alluvial.R
    View file
    Original file line number Diff line number Diff line change
    @@ -20,12 +20,28 @@ input_data
    # 10 chrX:1800-2000 8 8 8
    # … with 855,146 more rows

    # transform data into alluvial shape using the `to_lodes_form()` function
    transition_lodes <- input_data %>%
    # group counts by experimental groups
    input_data_grouped <- input_data %>%
    group_by(group1, group2, group3) %>%
    tally() %>%
    ungroup() %>%
    to_lodes_form(key = "test", axes = 1:3)
    tally()
    # A tibble: 265 x 4
    # Groups: group1, group2 [58]
    # group1 group2 group3 n
    # <fct> <fct> <fct> <int>
    # 1 1 1 1 703
    # 2 1 1 2 21
    # 3 1 1 3 14
    # 4 1 1 4 175
    # 5 1 1 5 4
    # 6 1 1 6 1
    # 7 1 1 8 14
    # 8 1 2 1 12
    # 9 1 2 2 2
    # 10 1 2 3 4
    # … with 255 more rows

    # transform data into alluvial shape using the `to_lodes_form()` function
    transition_lodes <- to_lodes_form(input_data_grouped, key = "test", axes = 1:3)
    # A tibble: 795 x 4
    # n alluvium test stratum
    # <int> <int> <fct> <fct>
  3. romanhaa revised this gist Feb 13, 2020. 1 changed file with 9 additions and 3 deletions.
    12 changes: 9 additions & 3 deletions alluvial.R
    View file
    Original file line number Diff line number Diff line change
    @@ -42,8 +42,14 @@ transition_lodes <- input_data %>%
    # … with 785 more rows

    # plot
    p <- transition_lodes %>%
    ggplot(aes(x = test, stratum = stratum, alluvium = alluvium,
    y = n, label = stratum)) +
    p <- ggplot(
    transition_lodes,
    aes(
    x = test,
    stratum = stratum,
    alluvium = alluvium,
    y = n
    )
    ) +
    geom_alluvium(aes(fill = stratum)) +
    geom_stratum(aes(fill = stratum))
  4. romanhaa created this gist Feb 13, 2020.
    49 changes: 49 additions & 0 deletions alluvial.R
    View file
    Original file line number Diff line number Diff line change
    @@ -0,0 +1,49 @@
    library("tidyverse")
    library("ggalluvial")

    # original data
    # every genomic bin of 200bp is assigned one of 8 possible chromatin states
    # note that group1-3 are factors
    input_data
    # A tibble: 855,156 x 4
    # bin group1 group2 group3
    # <chr> <fct> <fct> <fct>
    # 1 chrX:0-200 8 8 8
    # 2 chrX:200-400 8 8 8
    # 3 chrX:400-600 8 8 8
    # 4 chrX:600-800 8 8 8
    # 5 chrX:800-1000 8 8 8
    # 6 chrX:1000-1200 8 8 8
    # 7 chrX:1200-1400 8 8 8
    # 8 chrX:1400-1600 8 8 8
    # 9 chrX:1600-1800 8 8 8
    # 10 chrX:1800-2000 8 8 8
    # … with 855,146 more rows

    # transform data into alluvial shape using the `to_lodes_form()` function
    transition_lodes <- input_data %>%
    group_by(group1, group2, group3) %>%
    tally() %>%
    ungroup() %>%
    to_lodes_form(key = "test", axes = 1:3)
    # A tibble: 795 x 4
    # n alluvium test stratum
    # <int> <int> <fct> <fct>
    # 1 703 1 group1 1
    # 2 21 2 group1 1
    # 3 14 3 group1 1
    # 4 175 4 group1 1
    # 5 4 5 group1 1
    # 6 1 6 group1 1
    # 7 14 7 group1 1
    # 8 12 8 group1 1
    # 9 2 9 group1 1
    # 10 4 10 group1 1
    # … with 785 more rows

    # plot
    p <- transition_lodes %>%
    ggplot(aes(x = test, stratum = stratum, alluvium = alluvium,
    y = n, label = stratum)) +
    geom_alluvium(aes(fill = stratum)) +
    geom_stratum(aes(fill = stratum))