txviz

txviz is an R package for visualizing exon and intron structural differences between different transcripts.

Installation

# you can install the development version of txviz from GitHub:
# install.packages("devtools")
devtools::install_github("dzhang32/ggtranscript")
devtools::install_github("wwei-lab/txviz")

Usage

The four visualization methods implemented by txviz are used to show the differences between different transcripts, which are multi_gene()，samples_comp()，single_gene(),single_transcript().

Input data

To use txviz, you should provide:

• A reference gene annotation in GTF format,like Homo_sapiens.GRCh38.109.chr.gtf. Here we provide the filtered Homo_sapiens GRCh38.109.chr.gtf data, named the annotation.
• Several read annotation files for the reference genome, in Bed format.We provide several sample data with read annotations, named MUT1_read,MUT2_read,WT_read.
• A mapping file of transcirpt and read, which can be stored as data.frame data, needs to contain 'transcript_id' and 'name' columns, where the 'name' column represents 'readID'.Here we provide the mapping file,named the readmap.

multi_gene()

Drawing the transcript exon and intron structure of multiple genes at a large scale.

• Key Parameters

key parameter	description
annotation	A Gtf format data,imported into GRanges object.The data need to contain the column name of "transcript_id","gene_name","type","gene_id",etc.
read	A bed format data after alignment with the genome,imported into GRanges object.The data need to contain the column name of "name" as the readID.
readmap	A mapping file of transcirpt and read, which can be stored as data.frame data, needs to contain 'transcript_id' and 'name' columns, where the 'name' column represents 'readID'.
novel_transcript_ids	A dataframe with the column name needs to contain ‘novel_transcript_id’ to mark the color of novel isoform.
chr	The chromosome of interest,such as chr="6".
range	The range of interest,such as range=c(36000000,36700000).
strand	The strand of interest,such as strand="+" or "-" or "both";the default value is "both".
limit	To limit the number of read displays. If the read count exceeds the limit value, the limit+log2(read count-limit) number of reads will be randomly selected.

• Style Parameters

style parameter	description
read_low_color	The color is the minimum number of reads.
read_high_color	The color is the maximum number of reads.
annotation_color	The annotation exon color in the gtf format data.
novel_isoform_color	The annotation exon color in the gtf format data.
known_isoform_color	Mark the color of the known transcript isoform.
text_color	The font color of transcript name.
text_size	The font size of tittle name.
text_alpha	The font transparency of transcript name.
text_fontface	The font shape of transcript name.
title_color	The font color of tittle name.
title_size	The font size of tittle name.
title_face	The font shape of tittle name.
num_color	The font color of read number.
num_size	The font size of read number.
num_alpha	The font transparency of read number.
num_fontface	The font shape of read number.
num_margin	The read numbe moves to the left.
show_transcript_name	Whether the transcript name is displayed in the plot.The default is FALSE
x_text_size	The text size of x-axis.
x_text_just	Adjust the x-axis text position

• Output return a ggplot2 object
• Test Code

multi_gene(annotation,MUT1_read,readmap,chr='6',strand="both",range=c(36500000,36750000),limit=30,show_transcript_name=True)

samples_comp()

Comparison of transcript isoforms structural differences between multiple samples.

• Key Parameters

key parameter	description
annotation	A Gtf format data,imported into GRanges object.The data need to contain the column name of "transcript_id","gene_name","type","gene_id",etc.
readlist	A list object with the read data of multiple samples and the read data stored as GRanges object.The every read data need to contain the column name of "name" as the readID.
readmap	A mapping file of transcirpt and read, which can be stored as data.frame data, needs to contain 'transcript_id' and 'name' columns, where the 'name' column represents 'readID'.
interest_transcript_ids	A dataframe with the column name needs to contain 'interest_transcript_id' to choose what you want to show transcript isoform. The order of the interest transcript id is related to the order of the drawing
novel_transcript_ids	A dataframe with the column name needs to contain 'novel_transcript_id' to mark the color of novel isoform.
limit	To limit the number of read displays. If the read count exceeds the limit value, the limit+log2(read count-limit) number of reads will be randomly selected.

• Style Parameters

style parameter	description
text_color	The font color of transcript name.
text_size	The font size of tittle name.
text_alpha	The font transparency of transcript name.
text_fontface	The font shape of transcript name.
title_color	The font color of tittle name.
title_size	The font size of tittle name.
title_face	The font shape of tittle name.
num_color	The font color of read number.
num_size	The font size of read number.
num_alpha	The font transparency of read number.
num_fontface	The font shape of read number.
num_margin	The read numbe moves to the left.
show_transcript_name	Whether the transcript name is displayed in the plot.The default is FALSE
x_text_size	The text size of x-axis.

• Output

  return a ggplot2 object

• Test Code

#You need to name the elements in the list, which are related to the graph.
readlist=list("MUT1"=MUT1_read,"MUT2"=MUT2_read,"WT"=WT_read)
#The order of the interest transcript id is related to the order of the drawing.
interest_transcript_ids=data.frame(interest_transcript_id=c("ENST00000405375","ENST00000615513"))
samples_comp(annotation=annotation,readlist=readlist,readmap=readmap,limit=100,interest_transcript_ids=interest_transcript_ids)

single_gene()

Drawing the transcript exon and intron structure of a gene in the range.

• Key Parameters

key parameter	description
annotation	A Gtf format data,imported into GRanges object.The data need to contain the column name of "transcript_id","gene_name","type","gene_id",etc.
read	A bed format data after alignment with the genome,imported into GRanges object.The data need to contain the column name of "name" as the readID.
readmap	A mapping file of transcirpt and read, which can be stored as data.frame data, needs to contain 'transcript_id' and 'name' columns, where the 'name' column represents 'readID'.
chr	The chromosome of interest,such as chr="6".
range	The range of interest,such as range=c(36000000,36700000).
strand	The strand of interest,such as strand="+" or "-" or "both";the default value is "both".
limit	To limit the number of read displays. If the read count exceeds the limit value, the limit+log2(read count-limit) number of reads will be randomly selected.

• Style Parameters

style parameter	description
read_color	Displays the color of the read structure.
isoform_color	Displays the color of the transcript isoform structure
text_color	The font color of transcript name.
text_size	The font size of tittle name.
text_alpha	The font transparency of transcript name.
text_fontface	The font shape of transcript name.
title_color	The font color of tittle name.
title_size	The font size of tittle name.
title_face	The font shape of tittle name.
num_color	The font color of read number.
num_size	The font size of read number.
num_alpha	The font transparency of read number.
num_fontface	The font shape of read number.
num_margin	The read numbe moves to the left.
show_transcript_name	Whether the transcript name is displayed in the plot.The default is FALSE
x_text_size	The text size of x-axis.

• Output

  return a list object with ggplot2.

• Test Code

#
p_list=single_gene(annotation,MUT1_read,readmap,chr='6',strand="+",range=c(36050000,36700000),show_transcript_name=TRUE)
p_list[[1]]

single_transcript()

Drawing the exon and intron structure of interest transcript isoform.

• Key Parameters

key parameter	description
annotation	A Gtf format data,imported into GRanges object.The data need to contain the column name of "transcript_id","gene_name","type","gene_id",etc.
read	A bed format data after alignment with the genome,imported into GRanges object.The data need to contain the column name of "name" as the readID.
readmap	A mapping file of transcirpt and read, which can be stored as data.frame data, needs to contain 'transcript_id' and 'name' columns, where the 'name' column represents 'readID'.
interest_transcript_id	A string data as the interest transcript_id.
limit	To limit the number of read displays. If the read count exceeds the limit value, the limit+log2(read count-limit) number of reads will be randomly selected.

• Style Parameters

style parameter	description
read_color	Displays the color of the read structure.
isoform_color	Displays the color of the transcript isoform structure
title_color	The font color of tittle name.
title_size	The font size of tittle name.
title_face	The font shape of tittle name.
num_size	The font size of read number.
show_transcript_name	Whether the transcript name is displayed in the plot.The default is FALSE
x_text_size	The text size of x-axis.

• Output

  return a ggplot2 object

• Test Code

#
single_transcript(annotation,MUT1_read,readmap,"ENST00000405375")