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diff --git a/LICENSE b/LICENSE
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+MIT License
+
+Copyright (c) 2023 CaoTianze
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
diff --git a/README.md b/README.md
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+# plotnineSeqSuite: a Python package for visualizing sequence data using ggplot2
+## Installation
+`pip install plotnineseqsuite`
+## Getting Started
+See [plotnineSeqSuite Documentation](https://caotianze.github.io/plotnineseqsuite/) 
+## Development environment 
+PyCharm 2022.1 (Community Edition) and Spyder version: 5.4.1  (conda)
+## Dependencies
+Python version: 3.10.9 64-bit    
+plotnine: 0.10.1
diff --git a/docs/accepted_input_formats.png b/docs/accepted_input_formats.png
diff --git a/docs/bar_accepted_input_formats.png b/docs/bar_accepted_input_formats.png
diff --git a/docs/bar_no_sequence_letter.png b/docs/bar_no_sequence_letter.png
diff --git a/docs/col_schemes.md b/docs/col_schemes.md
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+# color schemes
+Default color schemes: chemistry, chemistry2, hydrophobicity, nucleotide, nucleotide2, base_pairing, clustalx, taylor.
+## *function* make_col_scheme(name: str = 'Custom Scheme', chars: Optional[list[str]] = None, groups: Optional[list[int]] = None, cols: Optional[list[int]] = None, values: Optional[list[int]] = None) -> dict
+```python
+from plotnineseqsuite.col_schemes import make_col_scheme
+cs1 = make_col_scheme(chars=['A', 'T', 'C', 'G'], groups=['gr1', 'gr1', 'gr2', 'gr2'],cols=['purple', 'purple', 'blue', 'blue'])
+cs2 = make_col_scheme(chars=['A', 'T', 'C', 'G'], values=[1,2,3,4])
+```
+The function is used to create custom color style themes.
+### name
+Name of custom scheme. It will display in legend.
+### chars
+Letters will used to plot.
+### groups
+Used in a custom discrete color scheme. It groups letters.
+### cols
+Used in a custom discrete color scheme. It represents the RGB value of the grouped color.
+### values
+Used in a custom continuous color scheme. It represents the numeric value of the corresponding letter.
+## *function* get_col_scheme(col_scheme: str, seq_type: str = 'AUTO') -> dict
+This function is used to get the built-in color theme of the type of the given sequence.
+```python
+from plotnineseqsuite.col_schemes import get_col_scheme
+col_df = get_col_scheme(col_scheme='chemistry')
+```
+### col_scheme
+One of the default color schemes.
+### seq_type
+AA or DNA or RNA
diff --git a/docs/combining_plots.png b/docs/combining_plots.png
diff --git a/docs/custom_alphabet.png b/docs/custom_alphabet.png
diff --git a/docs/custom_alphabet_2.png b/docs/custom_alphabet_2.png
diff --git a/docs/custom_color_schemes1.png b/docs/custom_color_schemes1.png
diff --git a/docs/custom_color_schemes2.png b/docs/custom_color_schemes2.png
diff --git a/docs/custom_height_logos.png b/docs/custom_height_logos.png
diff --git a/docs/font.md b/docs/font.md
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+# font
+Default fonts: times_new_roman, arial, courier_new, akrobat_bold, xkcd_regular, akrobat_regular, helvetica_bold, helvetica_light, helvetica_regular, roboto_bold, roboto_medium, roboto_regular, roboto_slab_bold, roboto_slab_light, roboto_slab_regular.
+## *function* list_fonts()
+Get all fonts.
+## *function* get_font(font_name: str) -> DataFrame
+```python
+from plotnineseqsuite import get_font
+f_df = get_font(font_name='times_new_roman')
+```
+Gets the specified font.
+### font_name
+Name of one of the default fonts.
diff --git a/docs/fonts.png b/docs/fonts.png
diff --git a/docs/geom_alignedSeq.md b/docs/geom_alignedSeq.md
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+# geom_alignedSeq
+A class that represents the sequence alignment diagram
+## *class* geom_alignedSeq(self,data: Union[list[str], dict, None] = None,seq_names: Optional[list[str]] = None,seq_type: str = 'AUTO',namespace: Optional[list[str]] = None,font: str = 'roboto_medium',stack_width: float = 0.75,font_col: str = '#FFFFFF',bg_col_scheme: Union[DataFrame, str] = 'AUTO',bg_low_col: str = 'black',bg_high_col: str = 'yellow',bg_na_col: str = '#333333',**kwargs: Any)
+```python
+from plotnine import ggplot, coord_fixed
+from plotnineseqsuite import geom_alignedSeq, theme_seq
+from plotnineseqsuite.data import seqs_dna
+ggplot() + geom_alignedSeq(seqs_dna['MA0013.1']) + theme_seq() + coord_fixed()
+```
+- data    
+Sequence data or corresponding dict.
+- seq_names    
+The name corresponding to the sequence data.
+- seq_type    
+OTHER, AA, DNA, RNA
+- namespace    
+The letter corresponding to the data. 
+- font    
+Font value
+- stack_width    
+The ratio of the size of letters to the standard unit width.
+- font_col    
+The color of the font.
+- bg_col_scheme    
+Color scheme of the backgrounds.
+- bg_low_col    
+Continuous color schemes are available.
+- bg_high_col    
+Continuous color schemes are available.
+- bg_na_col    
+Used when the background in the corresponding namespace do not have a color matching value defined.
+- kwargs    
+Other arguments passed on to layer().
+## *properties*
+- bg_data    
+DataFrame.
+- bg_layer    
+A geom_tile layer. Data come from the property bg_data.
+- letter_data    
+DataFrame.
+- letter_layer    
+A geom_polygon layer. Data come from the property letter_data.
+- scale_x_continuous    
+A custom scale_x_continuous.
+- scale_y_continuous    
+A custom scale_y_continuous.
+- xlab    
+A custom xlab.
+- ylab    
+A custom ylab.
+- colscale_opts    
+A custom scale_fill_gradient or custom scale_fill_manual.
diff --git a/docs/geom_logo.md b/docs/geom_logo.md
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+# geom_logo
+A class that represents the sequence logo
+## *class* geom_logo(self,data: Union[list[str], ndarray, dict, None] = None,method: str = 'bits',seq_type: str = 'AUTO',namespace: Optional[list[str]] = None,font: str = 'roboto_medium',stack_width: float = 0.95,rev_stack_order: bool = False,col_scheme: Union[DataFrame, str] = 'AUTO',low_col: str = 'black',high_col: str = 'yellow',na_col: str = '#333333',**kwargs: Any)
+```python
+from plotnine import ggplot
+from plotnineseqsuite import geom_logo, theme_seq
+from plotnineseqsuite.data import seqs_dna
+ggplot() + geom_logo(seqs_dna['MA0001.1']) + theme_seq()
+```
+- data    
+Sequence data or PFM or corresponding dict.
+- method    
+bits, probability, custom
+- seq_type    
+OTHER, AA, DNA, RNA
+- namespace    
+The letter corresponding to the data. If the type of data is ndarray, the order of the namespaces must correspond to that of ndarray.
+- font    
+Font value
+- stack_width    
+The ratio of the size of letters to the standard unit width.
+- rev_stack_order    
+Order of letter stack is reversed.
+- col_scheme    
+Color scheme of the letters.
+- low_col    
+Continuous color schemes are available.
+- high_col    
+Continuous color schemes are available.
+- na_col    
+Used when the letters in the corresponding namespace do not have a color matching value defined.
+- kwargs    	
+Other arguments passed on to layer().
+## *properties*
+- data    
+DataFrame.
+- layer    
+A geom_polygon layer. Data come from the property data.
+- scale_x_continuous    
+A custom scale_x_continuous.
+- xlab    
+A custom xlab.
+- ylab    
+A custom ylab.
+- colscale_opts    
+A custom scale_fill_gradient or custom scale_fill_manual.y
diff --git a/docs/geom_seqBar.md b/docs/geom_seqBar.md
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+# geom_seqBar
+A class that represents the sequence histogram
+## *class* geom_seqBar(self,data: Union[list[str], ndarray, dict, None] = None,seq_type: str = 'AUTO',namespace: Optional[list[str]] = None,font: str = 'roboto_medium',stack_width: float = 0.75,bar_col_scheme: Union[DataFrame, str] = 'AUTO',font_col: str = '#808080',low_col: str = 'black',high_col: str = 'yellow',na_col: str = '#333333',**kwargs: Any)
+```python
+from plotnine import ggplot
+from plotnineseqsuite import geom_seqBar, theme_seq
+from plotnineseqsuite.data import seqs_dna
+ggplot() + geom_seqBar(seqs_dna['MA0013.1']) + theme_seq()
+```
+- data    
+Sequence data or PFM or corresponding dict.
+- seq_type    
+OTHER, AA, DNA, RNA
+- namespace    
+The letter corresponding to the data. If the type of data is ndarray, the order of the namespaces must correspond to that of ndarray.
+- font    
+Font value
+- stack_width    
+The ratio of the size of letters and the width of  bars to the standard unit width.
+- bar_col_scheme    
+Color scheme of the cylinder.
+- font_col    
+The color of the font.
+- low_col    
+Continuous color schemes are available.
+- high_col    
+Continuous color schemes are available.
+- na_col    
+Used when the letters in the corresponding namespace do not have a color matching value defined.
+- kwargs    
+Other arguments passed on to layer().
+## *properties*
+- bar_data    
+DataFrame. 
+- bar_layer    
+A geom_tile layer. Data come from the property bar_data.
+- letter_data    
+DataFrame. 
+- letter_layer    
+A geom_polygon layer. Data come from the property letter_data.
+- scale_x_continuous    
+A custom scale_x_continuous.
+- scale_y_continuous    
+A custom scale_y_continuous.
+- xlab    
+A custom xlab.
+- ylab    
+A custom ylab.
+- colscale_opts    
+A custom scale_fill_gradient or custom scale_fill_manual.