add citation

README.md

@@ -14,7 +14,7 @@
    * [Phylogenomics pipeline](#Phylogenomics-pipeline)
    * [Input formats](#input-formats)
    * [Output formats](#output-formats)
-
+   * [Citation](#citation)
 ## Quick start ##
 ```
 git clone https://github.com/zhangrengang/orthoindex.git
@@ -473,3 +473,6 @@ SOG3001: Angelica_sinensis|AS08G03434 Angelica_sinensis|AS08G03435 Apium_graveol
 SOG3002: Angelica_sinensis|AS10G01791 Apium_graveolens|Ag1G00857 Apium_graveolens|Ag6G02641 Aralia_elata|AE12G02379 Centella_asiatica|evm.TU.Scaffold_7.2680 Coriandrum_sativum|Cs06G01941 Coriandrum_sativum|Cs06G01943 Coriandrum_sativum|Cs09G00381 Daucus_carota|DCAR_001660 Daucus_carota|DCAR_029095 Panax_ginseng|GWHGBEIL023683.1 Panax_ginseng|GWHGBEIL043112.1 Panax_notoginseng|PN013453
 ...
 ```
+
+## Citation ##
+Zhang RG, Shang HY, Zhou MJ et. al. Robust identification of orthologous synteny with the Orthology Index and its applications in reconstructing the evolutionary history of plant genomes. bioRxiv, 2024 [http://doi.org/10.1101/2024.08.22.609065]

soi/__version__.py

@@ -1 +1 @@
-version = '1.0'
+version = '1.0.5'

soi/dot_plotter.py

@@ -317,7 +317,7 @@ def plot_blocks(blocks, outplots, ks=None, max_ks=None, ks_hist=False, ks_cmap=N
 			ylabelpad += ycsize * 0.75
 
 	# species label
-	chr_color, arm_color = "dimgrey", "grey"
+	chr_color, arm_color = "dimgrey", 'silver' #c0c0c0, "grey":808080
 	if xlabel:
 		ax.set_xlabel(xlabel, ha='center', fontsize=xsize, labelpad=xlabelpad)
 		ax.xaxis.set_label_position('top')