Issue about zooming specific region

[HLHsieh]

Hi Manish,

I couldn’t find a similar issue on the issue list, so apologies if I missed it.

I am trying to visualize a specific region (e.g., chr4:190050000-190100000) in the reference genome using plotsr. I expected the plot to focus solely on the specified region. Below are the steps I followed and the challenges I encountered:

• Default plot:
  I ran the command:

plotsr --sr outsyri.out --genomes genomes.txt -o plot1.png

This produced a full plot as shown:

• Zoomed plot:
  When I tried zooming into the region using:

plotsr --sr outsyri.out --genomes genomes.txt -o plot2.png --reg ref:chr4:190050000-190100000

The resulting plot was unexpected and looked like this:

• Alternative approach:
  To address this, I manually truncated the reference genome to the specific region (chr4:190050000-190100000) and re-ran plotsr:

Data details for the default plot and zoomed plot

First few rows of outsyri.out:

chr4	1	190065228	-	-	-	-	-	NOTAL1	-	NOTAL	-
chr4	190065229	190089528	-	-	ctg0	16521	40836	DUP2	-	DUP	copygain
chr4	190065229	190089528	-	-	ctg0	16521	40836	DUPAL2	DUP2	DUPAL	-
chr4	190065229	190093263	-	-	ctg0	2	28089	SYN1	-	SYN	-
chr4	190065229	190093263	-	-	ctg0	2	28089	SYNAL1	SYN1	SYNAL	-
chr4	190065382	190065384	AGC	A	ctg0	155	155	DEL2	SYN1	DEL	-
chr4	190065649	190065650	GC	G	ctg0	420	420	DEL3	SYN1	DEL	-
chr4	190065658	190065664	ACGCCTC	A	ctg0	428	428	DEL4	SYN1	DEL	-
chr4	190065855	190065855	G	GC	ctg0	619	620	INS5	SYN1	INS	-
chr4	190065982	190065982	A	G	ctg0	747	747	SNP6	SYN1	SNP	-

genomes.txt file:

#file	name	tags
chr4.fa	ref	lw:1.5
primary.fasta	query	lw:1.5

Could you please clarify if I missed something in the usage of the --reg parameter? I was expecting --reg to limit the plot to the specified region directly.

I would appreciate any advice of how to achieve this more efficiently.

Thank you so much for your help!

Best,
Hsin