Using msaR

Zach Charlop-Powers

2021-09-21

Basic Usage

msaR is a an htmlwidgets wrapper of the BioJS MSA viewer javascript library. msa will pass alignments to the BioJS MSA.

library(msaR)

# read some sequences from a Multiple sequence alignment file.
seqfile <- system.file("sequences","AHBA.aln", package="msaR")

# display the MSA.
msaR(seqfile, menu=F, overviewbox = F)
Label
.2.4.6.8.10.12.14.16.18.20.22.24.26.28.30.32.34.36.38.40.42.44.46.48.50.52.54.56.58.60.62.64.66.68.70.72.74.76.78.80.82.84.86.88.90.92.94.96.98.100.102.104.106.108.110.112.114.116.118.120.122.124.126.128.130.132.134.136.138.140.142.144.146.148.150.152.154.156.158.160.162.164.166.168.170.172.174.176.178.180.182.184.186.188.190.192.194.196.198.200.202.204.206.208.210.212.214.216.218.220.222.224.226.228.230.232.234.236.238.240.242.244.246.248.250.252.254.256.258.260.262.264.266.268.270.272.274.276.278.280.282.284.286.288.290.292.294.296.298.300.302.304.306.308.310.312.314.316.318.320.322.324.326.328.330.332.334.336.338.340.342.344.346.348.350.352.354.356.358.360.362.364.366.368.370.372.374.376.378.380.382.384.386.388.390.392.394.396.398.400.402.404.406.408.410.412.414.416.418.420.422.424.426.428.430.432.434.436.438.440.442.444.446.448.450.452.454.456.458.460.462.464.466.468.470.472.474.476.478.480.482.484.486.488.490.492.494.496.498.500.502.504.506.508.510.512.514.516.518.520.522.524.526.528.530.532.534.536.538.540.542.544.546.548.550.552.554.556.558.560.562.564.566.568.570.572.574.576.578.580.582.584.586.588.590.592.594.596.598.600.602.604.606.608.610.612.614.616.618.620.622.624.626.628.630.632.634.636.638.640.642.644.646.648.650.652.654.656.658.660.662.664.666.668.670.672.674.676.678.680.682.684.686.688.690.692.694.696.698.700.702.704.706.708.710.712.714.716.718.720.722.724.726.728.730.732.734.736.738.740.742.744.746.748.750.752.754.756.758.760.762.764.766.768.770.772.774.776.778.780.782.784.786.788.790.792.794.796.798.800.802.804.806.808.810.812.814.816.818.820.822.824.826.828.830.832.834.836.838.840.842.844.846.848.850.852.854.856.858.860.862.864.866.868.870.872.874.876.878.880.882.884.886.888.890.892.894.896.898.900.902.904.906.908.910.912.914.916.918.920.922.924.926.928.930.932.934.936.938.940.942.944.946.948.950.952.954.956.958.960.962.964.966.968.970.972.974.976.978.980.982.984.986.988.990.992.994.996.998.1000.1002.1004.1006.1008.1010.1012.1014.1016.1018.1020.1022.1024.1026.1028.1030.1032.1034.1036.1038.1040.1042.1044.1046.1048.1050.1052.1054.1056.1058.1060.1062.1064.1066.1068.1070.1072.1074.1076.1078.1080.1082.1084.1086.1088.1090.1092.1094.1096.1098.1100.1102.1104.1106.1108.1110.1112.1114.1116.1118.1120.1122.1124.1126.1128.1130.1132.1134.1136.1138.1140.1142.1144.1146.1148.1150.1152.1154.1156.1158.1160.1162.1164.1166.1168.1170.1172.1174.1176.1178.1180.1182.1184.1186.1188.1190.1192.1194.1196.1198.1200.1202.1204.1206.1208.1210.1212.1214.1216.1218.1220.1222.1224.1226.1228.1230.1232
Hygrocin_AHBA
Macbecin_AHBA
Ansatrienin_AHBA
Ansamitocin_AHBA
Divergolide_AHBA
Rubradirin_AHBA
Napthomycin_AHBA
Neoansalactam_AHBA
Ansalactam_AHBA
Arifamycini
Chaxamycin_AHBA

Customized MSAs

msaR(seqfile, menu=F, overviewbox = F)
Label
.2.4.6.8.10.12.14.16.18.20.22.24.26.28.30.32.34.36.38.40.42.44.46.48.50.52.54.56.58.60.62.64.66.68.70.72.74.76.78.80.82.84.86.88.90.92.94.96.98.100.102.104.106.108.110.112.114.116.118.120.122.124.126.128.130.132.134.136.138.140.142.144.146.148.150.152.154.156.158.160.162.164.166.168.170.172.174.176.178.180.182.184.186.188.190.192.194.196.198.200.202.204.206.208.210.212.214.216.218.220.222.224.226.228.230.232.234.236.238.240.242.244.246.248.250.252.254.256.258.260.262.264.266.268.270.272.274.276.278.280.282.284.286.288.290.292.294.296.298.300.302.304.306.308.310.312.314.316.318.320.322.324.326.328.330.332.334.336.338.340.342.344.346.348.350.352.354.356.358.360.362.364.366.368.370.372.374.376.378.380.382.384.386.388.390.392.394.396.398.400.402.404.406.408.410.412.414.416.418.420.422.424.426.428.430.432.434.436.438.440.442.444.446.448.450.452.454.456.458.460.462.464.466.468.470.472.474.476.478.480.482.484.486.488.490.492.494.496.498.500.502.504.506.508.510.512.514.516.518.520.522.524.526.528.530.532.534.536.538.540.542.544.546.548.550.552.554.556.558.560.562.564.566.568.570.572.574.576.578.580.582.584.586.588.590.592.594.596.598.600.602.604.606.608.610.612.614.616.618.620.622.624.626.628.630.632.634.636.638.640.642.644.646.648.650.652.654.656.658.660.662.664.666.668.670.672.674.676.678.680.682.684.686.688.690.692.694.696.698.700.702.704.706.708.710.712.714.716.718.720.722.724.726.728.730.732.734.736.738.740.742.744.746.748.750.752.754.756.758.760.762.764.766.768.770.772.774.776.778.780.782.784.786.788.790.792.794.796.798.800.802.804.806.808.810.812.814.816.818.820.822.824.826.828.830.832.834.836.838.840.842.844.846.848.850.852.854.856.858.860.862.864.866.868.870.872.874.876.878.880.882.884.886.888.890.892.894.896.898.900.902.904.906.908.910.912.914.916.918.920.922.924.926.928.930.932.934.936.938.940.942.944.946.948.950.952.954.956.958.960.962.964.966.968.970.972.974.976.978.980.982.984.986.988.990.992.994.996.998.1000.1002.1004.1006.1008.1010.1012.1014.1016.1018.1020.1022.1024.1026.1028.1030.1032.1034.1036.1038.1040.1042.1044.1046.1048.1050.1052.1054.1056.1058.1060.1062.1064.1066.1068.1070.1072.1074.1076.1078.1080.1082.1084.1086.1088.1090.1092.1094.1096.1098.1100.1102.1104.1106.1108.1110.1112.1114.1116.1118.1120.1122.1124.1126.1128.1130.1132.1134.1136.1138.1140.1142.1144.1146.1148.1150.1152.1154.1156.1158.1160.1162.1164.1166.1168.1170.1172.1174.1176.1178.1180.1182.1184.1186.1188.1190.1192.1194.1196.1198.1200.1202.1204.1206.1208.1210.1212.1214.1216.1218.1220.1222.1224.1226.1228.1230.1232
Hygrocin_AHBA
Macbecin_AHBA
Ansatrienin_AHBA
Ansamitocin_AHBA
Divergolide_AHBA
Rubradirin_AHBA
Napthomycin_AHBA
Neoansalactam_AHBA
Ansalactam_AHBA
Arifamycini
Chaxamycin_AHBA

Protein MSA

# read some sequences from a Multiple sequence alignment file.
proteinseqfile <- system.file("sequences","phosphoproteins.aln", package="msaR")

# loading AA with ape. Can also use Biostrings
proteins <- ape::read.FASTA(proteinseqfile, type="AA")
                            
# note the seqlogo will show up in your widget but 
# not the vignette static output
msaR(proteins, menu=F, overviewbox = F,  colorscheme = "clustal")
Label
.2.4.6.8.10.12.14.16.18.20.22.24.26.28.30.32.34.36.38.40.42.44.46.48.50.52.54.56.58.60.62.64.66.68.70.72.74.76.78.80.82.84.86.88.90.92.94.96.98.100.102.104.106.108.110.112.114.116.118.120.122.124.126.128.130.132.134.136.138.140.142.144.146.148.150.152.154.156.158.160.162.164.166.168.170.172.174.176.178.180.182.184.186.188.190.192.194.196.198.200.202.204.206.208.210.212.214.216.218.220.222.224.226.228.230.232.234.236.238.240.242.244.246.248.250.252.254.256.258.260.262.264.266.268.270.272.274.276.278.280.282.284.286.288.290.292.294.296.298.300.302.304.306
P0C569
O56773
P06747
Q5VKP1

Use as a Shiny widget

msaR can be used as a widget with the Shiny web application framework.

In ui.R

msaROutput("msa", width="100%")

In server.R

output$msa <- renderMsaR(
  msaR(seqfile)
)