update for revised paper

README.md

@@ -7,4 +7,6 @@ See [plotnineSeqSuite Documentation](https://caotianze.github.io/plotnineseqsuit
 PyCharm 2022.1 (Community Edition) and Spyder version: 5.4.1  (conda)
 ## Dependencies
 Python version: 3.10.9 64-bit    
-plotnine: 0.10.1
+plotnine: 0.12.2
+## Similar projects
+R package [ggmsa](https://github.com/YuLab-SMU/ggmsa) and [ggseqlogo](https://github.com/omarwagih/ggseqlogo)

compare/test_ggmsa.r

@@ -0,0 +1,12 @@
+library(ggseqlogo)
+library(Biostrings)
+data(ggseqlogo_sample)
+library(ggplot2)
+library(ggmsa)
+aastr=seqs_aa[['CSNK2A2']]
+names(aastr)=1:80
+seqstr = AAStringSet(aastr)
+
+A=seqlogo(seqstr, adaptive = TRUE)+ggtitle('C')
+A=A+theme(panel.grid=element_blank(),panel.background=element_rect(fill='white',color=NA),plot.background=element_rect(fill='white',color=NA),axis.ticks.x=element_blank())
+ggsave('Fig. 3C.png',width=7,height=7,dpi=300)

compare/test_ggseqlogo.r

@@ -0,0 +1,7 @@
+library(ggplot2)
+library(ggseqlogo)
+data(ggseqlogo_sample)
+
+A=ggplot() + geom_logo(seqs_aa[['CSNK2A2']], method = 'probability', col_scheme='chemistry')+ggtitle('B')+guides(fill=FALSE)
+A=A+theme(panel.grid=element_blank(),panel.background=element_rect(fill='white'),axis.ticks.x=element_blank())
+ggsave('Fig. 3B.png',width=7,height=7,dpi=300)

compare/test_plotnineSeqSuite.py

@@ -0,0 +1,8 @@
+from plotnine import ggplot, ggtitle, theme, guides, element_blank, element_rect
+from plotnineseqsuite.data import seqs_aa
+from plotnineseqsuite.logo import geom_logo
+
+A=ggplot() + geom_logo(seqs_aa['CSNK2A2'], method='probability', col_scheme='chemistry') + ggtitle('A')+ guides(fill=False)
+A=A+theme(panel_grid=element_blank(),panel_background=element_rect(fill='white'),axis_ticks_major_x=element_blank())
+
+A.save("Fig. 3A.png",width=7,height=7,dpi=300)

plotnineseqsuite/align.py

@@ -133,10 +133,11 @@ def __radd__(self, gg):
                                  mapping=aes(x='x', y='y', width='width', height='height', fill='group'),
                                  **self.__kwargs)
             params.append(bg_layer)
+            params.append(self.colscale_opts)
         if self.letter_data is not None:
             letter_layer = geom_polygon(data=self.letter_data, mapping=aes(x='x', y='y', group='group_by'),
                                         fill=self.__font_col, **self.__kwargs)
             params.append(letter_layer)
-        params.extend([self.scale_x_continuous, self.scale_y_continuous, self.ylab, self.xlab, self.colscale_opts])
+        params.extend([self.scale_x_continuous, self.scale_y_continuous, self.ylab, self.xlab])
         gg = gg + params
         return gg

setup.py

@@ -5,7 +5,7 @@
 
 setuptools.setup(
     name="plotnineseqsuite",
-    version="0.9.0",
+    version="0.9.1",
     author="Cao Tianze",
     author_email="[email protected]",
     description="A Python package for visualizing sequence data using ggplot2",
@@ -24,9 +24,9 @@
     ],
     packages=['plotnineseqsuite','plotnineseqsuite.font','plotnineseqsuite.data'],
     python_requires=">=3.10",
-    install_requires=['plotnine>=0.10.1'],
+    install_requires=['plotnine==0.12.2'],
     license="MIT",
-    keywords=['ggplot2', 'plotnine', 'Bioinformatics', 'Sequence logo'],
+    keywords=['ggplot2', 'plotnine', 'Bioinformatics tool', 'Sequence logo'],
     package_data={
         "": ["*.csv"]
     }