How to Visulaise Genes per sample (Text visualisation)

Question

[Kritika]

Hi I have character matrix . I want to visualize all gene per sample . That means my all genes will be visible with there sample name Is there any approach to do this

MED20_Average   Glycyrrhizic_acid_rep_1

YIPF2_Average   Glycyrrhizic_acid_rep_1

PISD    Glycyrrhizic_acid_rep_1

AURKAIP1    Glycyrrhizic_acid_rep_1

BCL7C   Glycyrrhizic_acid_rep_1

PTCRA_Average   Hydroxysafflor_yellow_A

VPS53_Average   Hydroxysafflor_yellow_A

PTPN9   Hydroxysafflor_yellow_A

PHC3_Average    Anhydroicaritin

SCCPDH_Average  Anhydroicaritin

SOCS2_Average   Anhydroicaritin

SP2_Average Anhydroicaritin

LMTK2   Anhydroicaritin

TIMM10B Anhydroicaritin

GEMIN8  Anhydroicaritin

ABHD17B Anhydroicaritin

ANKMY1_Average  Hyperoside

F11R_Average    Hyperoside

[GenoMax]

It is not clear exactly what you want to do? It appears that your list is already sorted on the second column. Where are the sample names?

Answer 1

[steve]

If I am allowed to post two answers, I just figured this one out and like it better

#!/usr/bin/env Rscript

# visualize a character matrix

# install.packages("DiagrammeR")
library("DiagrammeR")


data <- structure(list(gene = structure(c(8L, 18L, 10L, 3L, 4L, 11L, 
17L, 12L, 9L, 13L, 14L, 15L, 7L, 16L, 6L, 1L, 2L, 5L), 
.Label = c("ABHD17B", "ANKMY1_Average", "AURKAIP1", 
"BCL7C", "F11R_Average", "GEMIN8", "LMTK2", 
"MED20_Average", "PHC3_Average", "PISD", 
"PTCRA_Average", "PTPN9", "SCCPDH_Average", 
"SOCS2_Average", "SP2_Average", "TIMM10B", 
"VPS53_Average", "YIPF2_Average"), 
class = "factor"), 
sample = structure(c(2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 4L,4L),
.Label = c("Anhydroicaritin", "Glycyrrhizic_acid_rep_1", 
"Hydroxysafflor_yellow_A", "Hyperoside"), 
class = "factor")), 
.Names = c("gene","sample"),
class = "data.frame", row.names = c(NA, -18L))

head(data)
# gene                  sample
# 1 MED20_Average Glycyrrhizic_acid_rep_1
# 2 YIPF2_Average Glycyrrhizic_acid_rep_1
# 3          PISD Glycyrrhizic_acid_rep_1
# 4      AURKAIP1 Glycyrrhizic_acid_rep_1
# 5         BCL7C Glycyrrhizic_acid_rep_1
# 6 PTCRA_Average Hydroxysafflor_yellow_A


uniquenodes <- unique(c(as.character(data[["gene"]]), as.character(data[["sample"]])))
nodes <- create_node_df(n = length(uniquenodes), 
                        type = "number", 
                        label = uniquenodes)
edges <- create_edge_df(from = match(as.character(data[["sample"]]), uniquenodes), 
                        to = match(as.character(data[["gene"]]), uniquenodes), 
                        rel = "related")
g <- create_graph(nodes_df=nodes, 
                  edges_df=edges)
render_graph(g)
# devtools::install_github('rich-iannone/DiagrammeRsvg')
# install.packages("rsvg")
export_graph(g, "genes_diagram.png")

Output:

References

http://rich-iannone.github.io/DiagrammeR/ndfs_edfs.html

https://github.com/rich-iannone/DiagrammeR#using-data-frames-to-define-graphviz-graphs

[Kritika]

Hi @steve This is awesome but my data is getting overlap only way to solve this is circular visulisations

Answer 2

[steve]

Here is something that does what you request, in R

#!/usr/bin/env Rscript

# visualize a character matrix

library("ggplot2")
# install.packages("ggrepel")
library("ggrepel") # for spreading text labels on the plot

lines <- "
MED20_Average   Glycyrrhizic_acid_rep_1

YIPF2_Average   Glycyrrhizic_acid_rep_1

PISD    Glycyrrhizic_acid_rep_1

AURKAIP1    Glycyrrhizic_acid_rep_1

BCL7C   Glycyrrhizic_acid_rep_1

PTCRA_Average   Hydroxysafflor_yellow_A

VPS53_Average   Hydroxysafflor_yellow_A

PTPN9   Hydroxysafflor_yellow_A

PHC3_Average    Anhydroicaritin

SCCPDH_Average  Anhydroicaritin

SOCS2_Average   Anhydroicaritin

SP2_Average Anhydroicaritin

LMTK2   Anhydroicaritin

TIMM10B Anhydroicaritin

GEMIN8  Anhydroicaritin

ABHD17B Anhydroicaritin

ANKMY1_Average  Hyperoside

F11R_Average    Hyperoside

"

con <- textConnection(lines)
data <- read.delim(con, header = FALSE, sep = "")
close(con)

colnames(data) <- c("gene", "sample")

head(data)
# gene                  sample
# 1 MED20_Average Glycyrrhizic_acid_rep_1
# 2 YIPF2_Average Glycyrrhizic_acid_rep_1
# 3          PISD Glycyrrhizic_acid_rep_1
# 4      AURKAIP1 Glycyrrhizic_acid_rep_1
# 5         BCL7C Glycyrrhizic_acid_rep_1
# 6 PTCRA_Average Hydroxysafflor_yellow_A

str(data)
# 'data.frame': 18 obs. of  2 variables:
#     $ gene  : Factor w/ 18 levels "ABHD17B","ANKMY1_Average",..: 8 18 10 3 4 11 17 12 9 13 ...
# $ sample: Factor w/ 4 levels "Anhydroicaritin",..: 2 2 2 2 2 3 3 3 1 1 ...

ggplot(data = data, aes(y = as.numeric(gene), x = as.numeric(gene), label = gene)) + 
    geom_dotplot(alpha = 0) + 
    facet_grid(sample~.) + 
    coord_cartesian(ylim = c(max(as.numeric(data[["gene"]])) + 1, 0 )) +
    theme(
          axis.text.x=element_blank(),
          axis.text.y=element_blank(),
          axis.ticks=element_blank(),
          axis.title.x=element_blank(),
          axis.title.y=element_blank(),
          panel.grid.major=element_blank(),
          panel.grid.minor=element_blank(),
          ) +
    geom_text_repel(aes(y = 0, label = gene), show.legend = FALSE, segment.alpha = 0, force = 5) + 
    ggtitle("Genes per Sample")

Output:

[Kritika]

Hi Can i get some thing like this https://ibb.co/kvgDxG ( d3.js images of circular dendogram) in R as well

Answer 3

[Ram]

Hi, I think circos.track from circlize package will be quite useful for your request : https://www.rdocumentation.org/packages/dendextend/versions/1.6.0/topics/circlize_dendrogram