Creating Sankey or Alluvial plot and stopping the flow where the "next_node" and "next_x" value is "NA" in R

Question

I am trying to create a Sankey or Alluvial plot using the ggplot2 library in R to visualize the flow of nodes based on the provided CSV data. The data includes columns for 'x', 'node', 'next_x', and 'next_node'. I want to create a plot where the flow is determined by the 'node' and 'next_node' columns. Additionally, I want to exclude any flows where 'next_x' is "NA".

Here's a simplified version of the CSV data I'm working with:

x   node    next_x  next_node
Homo_sapiens    SLC35A1 Mus_musculus    SLC35A1
Homo_sapiens    RARS2   Mus_musculus    RARS2
Homo_sapiens    ORC3    Mus_musculus    ORC3
Homo_sapiens    AKIRIN2 Mus_musculus    AKIRIN2
Homo_sapiens    SPACA1  Mus_musculus    SPACA1
Homo_sapiens    CNR1    Mus_musculus    CNR1
Homo_sapiens    RNGTT   Mus_musculus    RNGTT
Homo_sapiens    PNRC1   Mus_musculus    PNRC1
Homo_sapiens    PM20D2  Mus_musculus    PM20D2
Homo_sapiens    SRSF12  Mus_musculus    SRSF12
Homo_sapiens    GABRR1  Mus_musculus    GABRR1
Mus_musculus    GABRR1  Rattus_norvegicus   GABRR1
Mus_musculus    PM20D2  Rattus_norvegicus   PM20D2
Mus_musculus    SRSF12  Rattus_norvegicus   SRSF12
Mus_musculus    PNRC1   Rattus_norvegicus   PNRC1
Mus_musculus    RNGTT   Rattus_norvegicus   RNGTT
Mus_musculus    CNR1    Rattus_norvegicus   CNR1
Mus_musculus    SPACA1  Rattus_norvegicus   SPACA1
Mus_musculus    AKIRIN2 Rattus_norvegicus   AKIRIN2
Mus_musculus    ORC3    Rattus_norvegicus   ORC3
Mus_musculus    RARS2   Rattus_norvegicus   RARS2
Mus_musculus    SLC35A1 Rattus_norvegicus   SLC35A1
Rattus_norvegicus   GABRR1  Canis_lupus_familiaris  GABRR1
Rattus_norvegicus   PM20D2  Canis_lupus_familiaris  PM20D2
Rattus_norvegicus   SRSF12  Canis_lupus_familiaris  SRSF12
Rattus_norvegicus   PNRC1   Canis_lupus_familiaris  PNRC1
Rattus_norvegicus   RNGTT   Canis_lupus_familiaris  RNGTT
Rattus_norvegicus   CNR1    Canis_lupus_familiaris  CNR1
Rattus_norvegicus   SPACA1  Canis_lupus_familiaris  SPACA1
Rattus_norvegicus   AKIRIN2 Canis_lupus_familiaris  AKIRIN2
Rattus_norvegicus   ORC3    Canis_lupus_familiaris  ORC3
Rattus_norvegicus   RARS2   Canis_lupus_familiaris  RARS2
Rattus_norvegicus   SLC35A1 Canis_lupus_familiaris  SLC35A1
Canis_lupus_familiaris  SLC35A1 Monodelphis_domestica   SLC35A1
Canis_lupus_familiaris  RARS2   Monodelphis_domestica   RARS2
Canis_lupus_familiaris  ORC3    Monodelphis_domestica   ORC3
Canis_lupus_familiaris  AKIRIN2 Monodelphis_domestica   AKIRIN2
Canis_lupus_familiaris  SPACA1  Monodelphis_domestica   SPACA1
Canis_lupus_familiaris  CNR1    Monodelphis_domestica   CNR1
Canis_lupus_familiaris  RNGTT   Monodelphis_domestica   RNGTT
Canis_lupus_familiaris  PNRC1   Monodelphis_domestica   PNRC1
Canis_lupus_familiaris  SRSF12  Monodelphis_domestica   SRSF12
Canis_lupus_familiaris  PM20D2  Monodelphis_domestica   PM20D2
Canis_lupus_familiaris  GABRR1  Monodelphis_domestica   GABRR1
Monodelphis_domestica   SLC35A1 Ornithorhynchus_anatinus    SLC35A1
Monodelphis_domestica   RARS2   Ornithorhynchus_anatinus    RARS2
Monodelphis_domestica   ORC3    Ornithorhynchus_anatinus    ORC3
Monodelphis_domestica   AKIRIN2 Ornithorhynchus_anatinus    AKIRIN2
Monodelphis_domestica   SPACA1  Ornithorhynchus_anatinus    SPACA1
Monodelphis_domestica   CNR1    Ornithorhynchus_anatinus    CNR1
Monodelphis_domestica   RNGTT   Ornithorhynchus_anatinus    RNGTT
Monodelphis_domestica   PNRC1   Ornithorhynchus_anatinus    PNRC1
Monodelphis_domestica   SRSF12  NA  NA
Monodelphis_domestica   PM20D2  Ornithorhynchus_anatinus    PM20D2
Monodelphis_domestica   GABRR1  NA  NA
Ornithorhynchus_anatinus    SLC35A1 Gallus_gallus   SLC35A1
Ornithorhynchus_anatinus    RARS2   Gallus_gallus   RARS2
Ornithorhynchus_anatinus    ORC3    Gallus_gallus   ORC3
Ornithorhynchus_anatinus    AKIRIN2 Gallus_gallus   AKIRIN2
Ornithorhynchus_anatinus    SPACA1  Gallus_gallus   SPACA1
Ornithorhynchus_anatinus    CNR1    Gallus_gallus   CNR1
Ornithorhynchus_anatinus    RNGTT   Gallus_gallus   RNGTT
Ornithorhynchus_anatinus    PNRC1   Gallus_gallus   PNRC1
Ornithorhynchus_anatinus    PM20D2  Gallus_gallus   PM20D2
Ornithorhynchus_anatinus    LOC100076186    NA  NA
Ornithorhynchus_anatinus    LOC114805750    NA  NA
Gallus_gallus   PM20D2  Taeniopygia_guttata PM20D2
Gallus_gallus   PNRC1   Taeniopygia_guttata PNRC1
Gallus_gallus   BORCS6  Taeniopygia_guttata BORCS6
Gallus_gallus   RNGTT   Taeniopygia_guttata RNGTT
Gallus_gallus   LOC101749895    NA  NA
Gallus_gallus   CNR1    Taeniopygia_guttata CNR1
Gallus_gallus   SPACA1  NA  NA
Gallus_gallus   AKIRIN2 Taeniopygia_guttata AKIRIN2
Gallus_gallus   ORC3    Taeniopygia_guttata ORC3
Gallus_gallus   RARS2   Taeniopygia_guttata RARS2
Gallus_gallus   SLC35A1 Taeniopygia_guttata SLC35A1
Taeniopygia_guttata CFAP206 NA  NA
Taeniopygia_guttata SLC35A1 Chelonia_mydas  SLC35A1
Taeniopygia_guttata RARS2   Chelonia_mydas  RARS2
Taeniopygia_guttata ORC3    Chelonia_mydas  ORC3
Taeniopygia_guttata AKIRIN2 Chelonia_mydas  AKIRIN2
Taeniopygia_guttata CNR1    Chelonia_mydas  CNR1
Taeniopygia_guttata RNGTT   Chelonia_mydas  RNGTT
Taeniopygia_guttata BORCS6  NA  NA
Taeniopygia_guttata PNRC1   Chelonia_mydas  PNRC1
Taeniopygia_guttata PM20D2  Chelonia_mydas  PM20D2
Taeniopygia_guttata GABRR1  Chelonia_mydas  GABRR1
Chelonia_mydas  SLC35A1 Anolis_carolinensis SLC35A1
Chelonia_mydas  RARS2   Anolis_carolinensis RARS2
Chelonia_mydas  ORC3    Anolis_carolinensis ORC3
Chelonia_mydas  AKIRIN2 Anolis_carolinensis AKIRIN2
Chelonia_mydas  SPACA1  Anolis_carolinensis SPACA1
Chelonia_mydas  CNR1    Anolis_carolinensis CNR1
Chelonia_mydas  RNGTT   Anolis_carolinensis RNGTT
Chelonia_mydas  LOC102938330    NA  NA
Chelonia_mydas  PNRC1   Anolis_carolinensis PNRC1
Chelonia_mydas  PM20D2  Anolis_carolinensis PM20D2
Chelonia_mydas  GABRR1  NA  NA
Anolis_carolinensis PM20D2  NA  NA
Anolis_carolinensis SRSF12  NA  NA
Anolis_carolinensis PNRC1   NA  NA
Anolis_carolinensis RNGTT   NA  NA
Anolis_carolinensis LOC107982676    NA  NA
Anolis_carolinensis CNR1    NA  NA
Anolis_carolinensis SPACA1  NA  NA
Anolis_carolinensis AKIRIN2 NA  NA
Anolis_carolinensis ORC3    NA  NA
Anolis_carolinensis RARS2   NA  NA
Anolis_carolinensis SLC35A1 NA  NA
Xenopus_laevis  GABRR2.S    NA  NA
Xenopus_laevis  GABRR1.S    NA  NA
Xenopus_laevis  PM20D2.S    NA  NA
Xenopus_laevis  LOC108717975    NA  NA
Xenopus_laevis  RNGTT.S NA  NA
Xenopus_laevis  CNR1.S  NA  NA
Xenopus_laevis  AKIRIN2.S   NA  NA
Xenopus_laevis  ORC3.S  NA  NA
Xenopus_laevis  RARS2.S NA  NA
Xenopus_laevis  SLC35A1.S   NA  NA
Xenopus_laevis  LOC108717977    NA  NA
Latimeria_chalumnae DDX24   NA  NA
Latimeria_chalumnae PPP4R4  NA  NA
Latimeria_chalumnae SERPINA10B  NA  NA
Latimeria_chalumnae ARRDC3A NA  NA
Latimeria_chalumnae LOC102360869    NA  NA
Latimeria_chalumnae CNR1    Protopterus_annectens   CNR1
Latimeria_chalumnae SPACA1  NA  NA
Latimeria_chalumnae AKIRIN2 NA  NA
Latimeria_chalumnae ORC3    NA  NA
Latimeria_chalumnae RARS2   NA  NA
Latimeria_chalumnae LOC102362557    NA  NA
Protopterus_annectens   LOC122794922    NA  NA
Protopterus_annectens   LOC122794923    NA  NA
Protopterus_annectens   LOC122794924    NA  NA
Protopterus_annectens   FBXL5   NA  NA
Protopterus_annectens   CC2D2A  NA  NA
Protopterus_annectens   CNR1    Danio_rerio CNR1
Protopterus_annectens   CPEB2   NA  NA
Protopterus_annectens   BOD1L1  NA  NA
Protopterus_annectens   C1QTNF7 NA  NA
Protopterus_annectens   NKX3-2  NA  NA
Protopterus_annectens   RAB28   NA  NA
Danio_rerio MYO6A   NA  NA
Danio_rerio LOC569340   NA  NA
Danio_rerio MEI4    NA  NA
Danio_rerio NT5E    NA  NA
Danio_rerio SNX14   NA  NA
Danio_rerio CNR1    Oreochromis_niloticus   CNR1
Danio_rerio RNGTT   Oreochromis_niloticus   RNGTT
Danio_rerio PNRC1   NA  NA
Danio_rerio GABRR1  NA  NA
Danio_rerio GABRR2B NA  NA
Danio_rerio UBE2J1  NA  NA
Oreochromis_niloticus   SI:DKEY-174M14.3    NA  NA
Oreochromis_niloticus   RDH14B  NA  NA
Oreochromis_niloticus   LOC102078481    NA  NA
Oreochromis_niloticus   RNGTT   Scyliorhinus_canicula   RNGTT
Oreochromis_niloticus   LOC112842425    NA  NA
Oreochromis_niloticus   CNR1    Scyliorhinus_canicula   CNR1
Oreochromis_niloticus   AKIRIN2 Scyliorhinus_canicula   AKIRIN2
Oreochromis_niloticus   RARS2   Scyliorhinus_canicula   RARS2
Oreochromis_niloticus   SLC35A1 Scyliorhinus_canicula   SLC35A1
Oreochromis_niloticus   LOC100692709    NA  NA
Oreochromis_niloticus   LOC102081816    NA  NA
Scyliorhinus_canicula   SLC35A1 Petromyzon_marinus  SLC35A1
Scyliorhinus_canicula   RARS2   Petromyzon_marinus  RARS2
Scyliorhinus_canicula   ORC3    Petromyzon_marinus  ORC3
Scyliorhinus_canicula   AKIRIN2 Petromyzon_marinus  AKIRIN2
Scyliorhinus_canicula   LOC119967921    NA  NA
Scyliorhinus_canicula   CNR1    Petromyzon_marinus  CNR1
Scyliorhinus_canicula   RNGTT   Petromyzon_marinus  RNGTT
Scyliorhinus_canicula   LOC119967175    NA  NA
Scyliorhinus_canicula   PNRC1   NA  NA
Scyliorhinus_canicula   LOC119967178    NA  NA
Scyliorhinus_canicula   LOC119967180    NA  NA
Petromyzon_marinus  LOC116953416    NA  NA
Petromyzon_marinus  LOC116953419    NA  NA
Petromyzon_marinus  CEP162  NA  NA
Petromyzon_marinus  FBXL22  NA  NA
Petromyzon_marinus  RNGTT   NA  NA
Petromyzon_marinus  CNR1    NA  NA
Petromyzon_marinus  AKIRIN2 NA  NA
Petromyzon_marinus  ORC3    NA  NA
Petromyzon_marinus  RARS2   NA  NA
Petromyzon_marinus  SLC35A1 NA  NA
Petromyzon_marinus  RHBDL2  NA  NA

I'm using the ggplot2 library to create the plot, and I've tried the following script:

library(ggplot2)

pl <- ggplot(data, aes(x = x, node = node, next_node = next_node, next_x = next_x, fill = factor(node), label = node)) +
    geom_sankey(flow.alpha = 0.5,
                node.color = "black",
                show.legend = FALSE,
                na.rm = TRUE) +
    geom_sankey_label(size = 3, color = "black", fill="white", hjust = 0.5) +
    theme_bw() +
    theme(legend.position = "none") +
    theme(axis.title = element_blank(),
          axis.text.y = element_blank(),
          axis.ticks = element_blank(),
          panel.grid = element_blank()) +
    scale_fill_viridis_d(option = "inferno") +
    labs(title = "Sankey diagram using ggplot",
         fill = "Nodes")

However, when I run this script, I'm encountering the following warning messages:

Warning messages:
1: There was 1 warning in `dplyr::mutate()`.
ℹ In argument: `dplyr::across(c(x, next_x), ~as.numeric(.), .names = ("n_{.col}"))`.
Caused by warning:
! NAs introduced by coercion 
2: There was 1 warning in `dplyr::mutate()`.
ℹ In argument: `dplyr::across(c(x, next_x), ~as.numeric(.), .names = ("n_{.col}"))`.
Caused by warning:
! NAs introduced by coercion 
3: There was 1 warning in `dplyr::mutate()`.
ℹ In argument: `dplyr::across(c(x, next_x), ~as.numeric(.), .names = ("n_{.col}"))`.
Caused by warning:
! NAs introduced by coercion

I also get an incomplete plot:

Incomplete Sankey plot without flow

I'm seeking guidance on how to address this issue and successfully create the desired Sankey or Alluvial plot using ggplot2. Specifically, I want to achieve the following:

Create a plot where the flow is based on 'node' and 'next_node'.
Exclude flows where 'next_x' is "NA".
Avoid the warning messages related to dplyr::mutate() and NAs.

Any assistance or insights into solving this problem would be greatly appreciated. Thank you in advance!

Edit:

This is my raw dataset of gene neighbors:

species gene    start   stop    orientation
Homo_sapiens    SLC35A1 1   2   1
Homo_sapiens    RARS2   2   3   -1
Homo_sapiens    ORC3    3   4   1
Homo_sapiens    AKIRIN2 4   5   -1
Homo_sapiens    SPACA1  5   6   1
Homo_sapiens    CNR1    6   7   -1
Homo_sapiens    RNGTT   7   8   -1
Homo_sapiens    PNRC1   8   9   1
Homo_sapiens    PM20D2  9   10  1
Homo_sapiens    SRSF12  10  11  -1
Homo_sapiens    GABRR1  11  12  -1
Mus_musculus    GABRR1  1   2   1
Mus_musculus    PM20D2  2   3   -1
Mus_musculus    SRSF12  3   4   1
Mus_musculus    PNRC1   4   5   -1
Mus_musculus    RNGTT   5   6   1
Mus_musculus    CNR1    6   7   1
Mus_musculus    SPACA1  7   8   -1
Mus_musculus    AKIRIN2 8   9   1
Mus_musculus    ORC3    9   10  -1
Mus_musculus    RARS2   10  11  1
Mus_musculus    SLC35A1 11  12  -1
Rattus_norvegicus   GABRR1  1   2   1
Rattus_norvegicus   PM20D2  2   3   -1
Rattus_norvegicus   SRSF12  3   4   1
Rattus_norvegicus   PNRC1   4   5   -1
Rattus_norvegicus   RNGTT   5   6   1
Rattus_norvegicus   CNR1    6   7   1
Rattus_norvegicus   SPACA1  7   8   -1
Rattus_norvegicus   AKIRIN2 8   9   1
Rattus_norvegicus   ORC3    9   10  -1
Rattus_norvegicus   RARS2   10  11  1
Rattus_norvegicus   SLC35A1 11  12  -1
Canis_lupus_familiaris  SLC35A1 1   2   1
Canis_lupus_familiaris  RARS2   2   3   -1
Canis_lupus_familiaris  ORC3    3   4   1
Canis_lupus_familiaris  AKIRIN2 4   5   -1
Canis_lupus_familiaris  SPACA1  5   6   1
Canis_lupus_familiaris  CNR1    6   7   -1
Canis_lupus_familiaris  RNGTT   7   8   -1
Canis_lupus_familiaris  PNRC1   8   9   1
Canis_lupus_familiaris  SRSF12  9   10  -1
Canis_lupus_familiaris  PM20D2  10  11  1
Canis_lupus_familiaris  GABRR1  11  12  -1
Monodelphis_domestica   SLC35A1 1   2   1
Monodelphis_domestica   RARS2   2   3   -1
Monodelphis_domestica   ORC3    3   4   1
Monodelphis_domestica   AKIRIN2 4   5   -1
Monodelphis_domestica   SPACA1  5   6   1
Monodelphis_domestica   CNR1    6   7   -1
Monodelphis_domestica   RNGTT   7   8   -1
Monodelphis_domestica   PNRC1   8   9   1
Monodelphis_domestica   SRSF12  9   10  -1
Monodelphis_domestica   PM20D2  10  11  1
Monodelphis_domestica   GABRR1  11  12  -1
Ornithorhynchus_anatinus    SLC35A1 1   2   1
Ornithorhynchus_anatinus    RARS2   2   3   -1
Ornithorhynchus_anatinus    ORC3    3   4   1
Ornithorhynchus_anatinus    AKIRIN2 4   5   -1
Ornithorhynchus_anatinus    SPACA1  5   6   1
Ornithorhynchus_anatinus    CNR1    6   7   -1
Ornithorhynchus_anatinus    RNGTT   7   8   -1
Ornithorhynchus_anatinus    PNRC1   8   9   1
Ornithorhynchus_anatinus    PM20D2  9   10  1
Ornithorhynchus_anatinus    LOC100076186    10  11  -1
Ornithorhynchus_anatinus    LOC114805750    11  12  1
Gallus_gallus   PM20D2  1   2   -1
Gallus_gallus   PNRC1   2   3   -1
Gallus_gallus   BORCS6  3   4   1
Gallus_gallus   RNGTT   4   5   1
Gallus_gallus   LOC101749895    5   6   1
Gallus_gallus   CNR1    6   7   1
Gallus_gallus   SPACA1  7   8   -1
Gallus_gallus   AKIRIN2 8   9   1
Gallus_gallus   ORC3    9   10  -1
Gallus_gallus   RARS2   10  11  1
Gallus_gallus   SLC35A1 11  12  -1
Taeniopygia_guttata CFAP206 1   2   1
Taeniopygia_guttata SLC35A1 2   3   1
Taeniopygia_guttata RARS2   3   4   -1
Taeniopygia_guttata ORC3    4   5   1
Taeniopygia_guttata AKIRIN2 5   6   -1
Taeniopygia_guttata CNR1    6   7   -1
Taeniopygia_guttata RNGTT   7   8   -1
Taeniopygia_guttata BORCS6  8   9   -1
Taeniopygia_guttata PNRC1   9   10  1
Taeniopygia_guttata PM20D2  10  11  1
Taeniopygia_guttata GABRR1  11  12  -1
Chelonia_mydas  SLC35A1 1   2   1
Chelonia_mydas  RARS2   2   3   -1
Chelonia_mydas  ORC3    3   4   1
Chelonia_mydas  AKIRIN2 4   5   -1
Chelonia_mydas  SPACA1  5   6   1
Chelonia_mydas  CNR1    6   7   -1
Chelonia_mydas  RNGTT   7   8   -1
Chelonia_mydas  LOC102938330    8   9   -1
Chelonia_mydas  PNRC1   9   10  1
Chelonia_mydas  PM20D2  10  11  1
Chelonia_mydas  GABRR1  11  12  -1
Anolis_carolinensis PM20D2  1   2   -1
Anolis_carolinensis SRSF12  2   3   1
Anolis_carolinensis PNRC1   3   4   -1
Anolis_carolinensis RNGTT   4   5   1
Anolis_carolinensis LOC107982676    5   6   -1
Anolis_carolinensis CNR1    6   7   1
Anolis_carolinensis SPACA1  7   8   -1
Anolis_carolinensis AKIRIN2 8   9   1
Anolis_carolinensis ORC3    9   10  -1
Anolis_carolinensis RARS2   10  11  1
Anolis_carolinensis SLC35A1 11  12  -1
Xenopus_laevis  GABRR2.S    1   2   1
Xenopus_laevis  GABRR1.S    2   3   1
Xenopus_laevis  PM20D2.S    3   4   -1
Xenopus_laevis  LOC108717975    4   5   1
Xenopus_laevis  RNGTT.S 5   6   1
Xenopus_laevis  CNR1.S  6   7   1
Xenopus_laevis  AKIRIN2.S   7   8   1
Xenopus_laevis  ORC3.S  8   9   -1
Xenopus_laevis  RARS2.S 9   10  1
Xenopus_laevis  SLC35A1.S   10  11  -1
Xenopus_laevis  LOC108717977    11  12  1
Latimeria_chalumnae DDX24   1   2   -1
Latimeria_chalumnae PPP4R4  2   3   1
Latimeria_chalumnae SERPINA10B  3   4   -1
Latimeria_chalumnae ARRDC3A 4   5   1
Latimeria_chalumnae LOC102360869    5   6   -1
Latimeria_chalumnae CNR1    6   7   1
Latimeria_chalumnae SPACA1  7   8   -1
Latimeria_chalumnae AKIRIN2 8   9   1
Latimeria_chalumnae ORC3    9   10  -1
Latimeria_chalumnae RARS2   10  11  1
Latimeria_chalumnae LOC102362557    11  12  1
Protopterus_annectens   LOC122794922    1   2   1
Protopterus_annectens   LOC122794923    2   3   1
Protopterus_annectens   LOC122794924    3   4   1
Protopterus_annectens   FBXL5   4   5   1
Protopterus_annectens   CC2D2A  5   6   -1
Protopterus_annectens   CNR1    6   7   1
Protopterus_annectens   CPEB2   7   8   -1
Protopterus_annectens   BOD1L1  8   9   -1
Protopterus_annectens   C1QTNF7 9   10  -1
Protopterus_annectens   NKX3-2  10  11  1
Protopterus_annectens   RAB28   11  12  1
Danio_rerio MYO6A   1   2   1
Danio_rerio LOC569340   2   3   -1
Danio_rerio MEI4    3   4   1
Danio_rerio NT5E    4   5   1
Danio_rerio SNX14   5   6   -1
Danio_rerio CNR1    6   7   -1
Danio_rerio RNGTT   7   8   -1
Danio_rerio PNRC1   8   9   1
Danio_rerio GABRR1  9   10  -1
Danio_rerio GABRR2B 10  11  -1
Danio_rerio UBE2J1  11  12  -1
Oreochromis_niloticus   SI:DKEY-174M14.3    1   2   1
Oreochromis_niloticus   RDH14B  2   3   -1
Oreochromis_niloticus   LOC102078481    3   4   1
Oreochromis_niloticus   RNGTT   4   5   1
Oreochromis_niloticus   LOC112842425    5   6   -1
Oreochromis_niloticus   CNR1    6   7   1
Oreochromis_niloticus   AKIRIN2 7   8   1
Oreochromis_niloticus   RARS2   8   9   1
Oreochromis_niloticus   SLC35A1 9   10  -1
Oreochromis_niloticus   LOC100692709    10  11  -1
Oreochromis_niloticus   LOC102081816    11  12  1
Scyliorhinus_canicula   SLC35A1 1   2   1
Scyliorhinus_canicula   RARS2   2   3   -1
Scyliorhinus_canicula   ORC3    3   4   1
Scyliorhinus_canicula   AKIRIN2 4   5   -1
Scyliorhinus_canicula   LOC119967921    5   6   1
Scyliorhinus_canicula   CNR1    6   7   -1
Scyliorhinus_canicula   RNGTT   7   8   -1
Scyliorhinus_canicula   LOC119967175    8   9   -1
Scyliorhinus_canicula   PNRC1   9   10  1
Scyliorhinus_canicula   LOC119967178    10  11  1
Scyliorhinus_canicula   LOC119967180    11  12  -1
Petromyzon_marinus  LOC116953416    1   2   -1
Petromyzon_marinus  LOC116953419    2   3   -1
Petromyzon_marinus  CEP162  3   4   1
Petromyzon_marinus  FBXL22  4   5   -1
Petromyzon_marinus  RNGTT   5   6   1
Petromyzon_marinus  CNR1    6   7   1
Petromyzon_marinus  AKIRIN2 7   8   1
Petromyzon_marinus  ORC3    8   9   -1
Petromyzon_marinus  RARS2   9   10  1
Petromyzon_marinus  SLC35A1 10  11  -1
Petromyzon_marinus  RHBDL2  11  12  1

Edit 2:

I've managed to get few flows connected but it is still incorrect. The problem is probably with the order of the rows. Can somebody please suggest something?

Allan Cameron · Answer 1 · 2023-08-03T22:24:48.420

1

It's not clear why you are trying to draw a Sankey diagram here. Each connection only has a single flow, and if you draw all the genes at the same height, all the connections are horizontal. It makes more sense and is tidier as a graph:

library(tidyverse)
library(tidygraph)
library(ggraph)

data.frame(from = paste(data[[1]], data[[2]]),
           to = paste(data[[3]], data[[4]])) %>%
  filter(to != "NA NA") %>%
  as_tbl_graph() %>%
  mutate(Species = str_replace(str_remove(name, " .*"), "_", "\n"),
         Gene    = str_remove(name, ".* "),
         ypos    = as.numeric(factor(Gene)),
         xpos     = as.numeric(factor(Species, unique(Species)))) %>%
  ggraph(layout = "manual", x = xpos, y = ypos) +
  geom_edge_fan(width = 4, alpha = 0.2) +
  geom_node_point(aes(fill = Gene), shape = 22, size = 12) +
  geom_node_label(aes(label = Gene), size = 2.5) +
  geom_text(aes(x = xpos, label = Species, y = 0), check_overlap = TRUE) +
  scale_fill_viridis_d(guide = "none") +
  scale_edge_color_viridis(guide = "none") +
  theme_void()

You could even just do it as a dot-and-line plot:

library(tidyverse)

levs <- names(sort(table(c(data$node, data$next_node))))

data %>%
  mutate(x = gsub("_", "\n", x), next_x = gsub("_", "\n", next_x)) %>%
  mutate(node = factor(node, levs), 
         next_node = factor(next_node, levs)) %>%
  ggplot(aes(x, node, color = node)) +
  geom_segment(aes(xend = next_x, yend = next_node), linewidth = 1) +
  geom_point(size = 2.5) +
  geom_point(aes(x = next_x, y = next_node), size = 2.5) +
  scale_color_viridis_d(guide = "none") +
  scale_y_discrete(limits = levs) +
  theme_minimal()

edited Aug 03 '23 at 22:24

answered Aug 03 '23 at 21:07

Allan Cameron

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I appreciate your feedback and understand your perspective. However, the intention behind using a Sankey diagram in this context is to showcase the synteny and gene conservation around the gene of interest "CNR1" throughout evolutionary history. By arranging the genes at the same height, the diagram allows us to clearly represent the connections between genes that are conserved. Is it possible to represent all the genes as well as keep the gene of interest CNR1 in the centre? – Rohan Nath Aug 03 '23 at 21:33
@RohanNath the problem with including all the genes is that the majority are singletons. They take up so much space that they make your plot pretty illegible and don't add much to the story you are trying to tell – Allan Cameron Aug 03 '23 at 22:27
I completely understand your concern about the potential clutter that including all the singleton genes might introduce to the plot. Maintaining visual clarity is indeed crucial for effective communication. However, in this specific case, the primary objective is to demonstrate the conservation of genomic arrangement and the relationships of neighboring genes with the gene of interest "CNR1." I've attached a reference link that explains the significance of this approach in more detail. Reference: https://www.science.org/doi/10.1126/sciadv.abi5884 (see fig. 1). That's what I'm aiming for. – Rohan Nath Aug 03 '23 at 22:40
I've added another image after much tweaking but it is incorrect. The issue seems to lie with the order of the rows. I would be grateful if you could suggest something. I've been stuck on this for days now. – Rohan Nath Aug 03 '23 at 22:47
@RohanNath it seems to me that the plot you are trying to emulate has a single thin line for each gene. Each line passes through a chromosome in each species. In terms of sankey / alluvial plots, the genes are the flows and the chromosomes are the nodes and the species are the axis breaks. To get a similar plot, you need an extra grouping variable (like chromosome number), and move away from labelling each gene. – Allan Cameron Aug 03 '23 at 22:51
I apologize if my previous explanations didn't fully convey the approach. In my visualization, I'm considering each individual gene as a node, with the gene of interest "CNR1" at the center. By representing the genes as nodes and using the flows to connect genes with the same name in various species, we effectively highlight the conservation of these genes throughout evolutionary history. I'm utilizing flows to demonstrate the connections between genes with the same name, showcasing their presence across different species. – Rohan Nath Aug 03 '23 at 23:05
@RohanNath I understand that, and it is what both my examples show. But my point is that if you are using Genes for nodes but also for flow, a Sankey diagram is probably the wrong choice. You need another grouping variable (such as chromosome) to emulate the plot in the linked paper. Also, some genes only appear in a single species, so they are only a single node and cannot have any flow anywhere else. Again, this doesn't work in a Sankey diagram. If you want all the genes and all the species, highlighting conservation, then a simple presence / absence heatmap might be best. – Allan Cameron Aug 04 '23 at 07:16
I've had a discussion with my PhD supervisor, and he too emphasized the importance of maintaining a clean and understandable plot. Additionally, he shared a reference diagram (https://ars.els-cdn.com/content/image/1-s2.0-S105579032030261X-gr2_lrg.jpg). In this diagram, genes are horizontally arranged, facing either side based on their orientation value. The connections between genes with the same name are represented by vertical arrows or lines. Considering this reference, I'm exploring the possibility of creating a similar plot using the DiagrammeR package in R. Is it possible? – Rohan Nath Aug 04 '23 at 08:43
@RohanNath there are many ways to plot the data you have, but what I would suggest is that you sketch out roughly what you would want the finished plot to look like, and ensure that you have enough information in your data to produce such a plot. You do need to take into account how much information you can include in your plot before it becomes illegible. However, questions about _how_ to present your data might be better asked over at [CrossValidated](https://stats.stackexchange.com) – Allan Cameron Aug 04 '23 at 11:17

Creating Sankey or Alluvial plot and stopping the flow where the "next_node" and "next_x" value is "NA" in R

1 Answers1